Plasmodium falciparum
Species | Prediction |
---|---|
Plasmodium falciparum |
99.76 |
3 tables.
1. Indicating drug resistant markers
2. Other variants encountered
3. Areas which were missing when analysing
4. Variants that failed the quality control report
NextDrug | Mutations |
---|---|
Chloroquine |
MDR1 p.Tyr184Phe (1.00) , CRT p.Lys76Thr (1.00) , CRT p.Gln271Glu (1.00) , CRT p.Ile356Thr (1.00) , CRT p.Arg371Ile (1.00) |
Mefloquine |
|
Pyrimethamine |
DHFR-TS p.Asn51Ile (1.00) , DHFR-TS p.Cys59Arg (1.00) , DHFR-TS p.Ser108Asn (1.00) , DHFR-TS p.Ile164Leu (1.00) |
Sulfadoxine |
PPPK-DHPS p.Ser436Ala (1.00) , PPPK-DHPS p.Ala437Gly (1.00) |
Artemisinin |
Chromosome: | Genome Position | Locus Tag | Gene Name | Change | Estimated fraction |
---|---|---|---|---|---|
Pf3D7_01_v3 | 190143 | PF3D7_0104300 | UBP1 | c.-126_-125insAT | 1.0 |
Pf3D7_01_v3 | 190260 | PF3D7_0104300 | UBP1 | c.-9G>A | 0.96 |
Pf3D7_01_v3 | 190616 | PF3D7_0104300 | UBP1 | c.348A>G | 1.0 |
Pf3D7_01_v3 | 191282 | PF3D7_0104300 | UBP1 | c.1014C>T | 0.41 |
Pf3D7_01_v3 | 191685 | PF3D7_0104300 | UBP1 | c.1444_1446delAAT | 0.95 |
Pf3D7_01_v3 | 192111 | PF3D7_0104300 | UBP1 | p.Tyr615His | 1.0 |
Pf3D7_01_v3 | 192633 | PF3D7_0104300 | UBP1 | p.Asn789Asp | 1.0 |
Pf3D7_01_v3 | 193167 | PF3D7_0104300 | UBP1 | p.Met967Val | 0.96 |
Pf3D7_01_v3 | 193299 | PF3D7_0104300 | UBP1 | p.Glu1011Lys | 0.97 |
Pf3D7_01_v3 | 193667 | PF3D7_0104300 | UBP1 | p.Arg1133Ser | 1.0 |
Pf3D7_01_v3 | 194117 | PF3D7_0104300 | UBP1 | c.3849T>C | 1.0 |
Pf3D7_01_v3 | 194843 | PF3D7_0104300 | UBP1 | c.4593_4601delAAAATATGA | 0.67 |
Pf3D7_01_v3 | 194843 | PF3D7_0104300 | UBP1 | c.4593_4601delAAAATATGA | 0.67 |
Pf3D7_01_v3 | 196010 | PF3D7_0104300 | UBP1 | p.Lys1914Asn | 0.78 |
Pf3D7_01_v3 | 196011 | PF3D7_0104300 | UBP1 | p.Glu1915Lys | 0.77 |
Pf3D7_01_v3 | 196981 | PF3D7_0104300 | UBP1 | p.Arg2238Lys | 1.0 |
Pf3D7_01_v3 | 201154 | PF3D7_0104300 | UBP1 | p.Leu3475Ser | 1.0 |
Pf3D7_03_v3 | 922867 | PF3D7_0321900 | CARL | c.-106_-105delAT | 1.0 |
Pf3D7_03_v3 | 924907 | PF3D7_0321900 | CARL | c.1806G>T | 1.0 |
Pf3D7_03_v3 | 925808 | PF3D7_0321900 | CARL | p.Lys903Glu | 1.0 |
Pf3D7_03_v3 | 925890 | PF3D7_0321900 | CARL | c.2804_2809delATAATA | 1.0 |
Pf3D7_03_v3 | 925967 | PF3D7_0321900 | CARL | p.Glu956Lys | 1.0 |
Pf3D7_05_v3 | 410184 | PF3D7_0509800 | PI4K | c.-84C>A | 1.0 |
Pf3D7_05_v3 | 410338 | PF3D7_0509800 | PI4K | p.His24Leu | 1.0 |
Pf3D7_05_v3 | 410566 | PF3D7_0509800 | PI4K | p.Val100Ala | 1.0 |
Pf3D7_05_v3 | 412910 | PF3D7_0509800 | PI4K | c.2646_2649delCAACinsTAAT | 0.5 |
Pf3D7_05_v3 | 413414 | PF3D7_0509800 | PI4K | c.3147T>C | 0.56 |
Pf3D7_05_v3 | 959840 | PF3D7_0523000 | MDR1 | p.Asp651Asn | 0.43 |
Pf3D7_07_v3 | 403620 | PF3D7_0709000 | CRT | p.MetAsn74IleAsp | 1.0 |
Pf3D7_07_v3 | 403623 | PF3D7_0709000 | CRT | p.Asn75Lys | 1.0 |
Pf3D7_08_v3 | 643648 | PF3D7_0813000 | PF3D7_0813000 | p.Ser413Asn | 0.49 |
Pf3D7_08_v3 | 644936 | PF3D7_0813000 | PF3D7_0813000 | c.-51C>A | 1.0 |
Pf3D7_10_v3 | 1045876 | PF3D7_1025000 | PF3D7_1025000 | p.Gln932Glu | 1.0 |
Pf3D7_10_v3 | 1046056 | PF3D7_1025000 | PF3D7_1025000 | c.2724C>G | 1.0 |
Pf3D7_10_v3 | 1047323 | PF3D7_1025000 | PF3D7_1025000 | p.Phe486Ser | 1.0 |
Pf3D7_10_v3 | 1047391 | PF3D7_1025000 | PF3D7_1025000 | c.1383A>G | 0.65 |
Pf3D7_10_v3 | 1047391 | PF3D7_1025000 | PF3D7_1025000 | c.1383A>G | 0.65 |
Pf3D7_10_v3 | 1049903 | PF3D7_1025000 | PF3D7_1025000 | c.-145_-144delAT | 0.94 |
Pf3D7_10_v3 | 1449646 | PF3D7_1036800 | PF3D7_1036800 | p.Thr459Ile | 1.0 |
Pf3D7_11_v3 | 1526106 | PF3D7_1138700 | PF3D7_1138700 | p.Ser1721Ala | 1.0 |
Pf3D7_11_v3 | 1529369 | PF3D7_1138700 | PF3D7_1138700 | p.Ser633Asn | 0.8 |
Pf3D7_11_v3 | 1529778 | PF3D7_1138700 | PF3D7_1138700 | p.Glu497Gln | 1.0 |
Pf3D7_11_v3 | 1530261 | PF3D7_1138700 | PF3D7_1138700 | p.Glu336Gln | 1.0 |
Pf3D7_12_v3 | 211053 | PF3D7_1204400 | PF3D7_1204400 | c.-162_-161delAT | 1.0 |
Pf3D7_12_v3 | 529418 | PF3D7_1211900 | ATP4 | p.Gly1128Arg | 1.0 |
Pf3D7_12_v3 | 532131 | PF3D7_1211900 | ATP4 | c.669C>A | 1.0 |
Pf3D7_12_v3 | 532889 | PF3D7_1211900 | ATP4 | c.-98_-91delATCTATAT | 1.0 |
Pf3D7_12_v3 | 591301 | PF3D7_1213800 | PRS | c.1134A>G | 1.0 |
Pf3D7_12_v3 | 592329 | PF3D7_1213800 | PRS | p.Val36Ile | 1.0 |
Pf3D7_12_v3 | 592496 | PF3D7_1213800 | PRS | c.-62G>A | 1.0 |
Pf3D7_12_v3 | 718631 | PF3D7_1218300 | AP2-MU | c.699_701delTAA | 1.0 |
Pf3D7_12_v3 | 1927229 | PF3D7_1246300 | PF3D7_1246300 | c.1041T>C | 1.0 |
Pf3D7_12_v3 | 2093058 | PF3D7_1251200 | PF3D7_1251200 | c.636A>G | 1.0 |
Pf3D7_13_v3 | 1726571 | PF3D7_1343700 | K13 | c.421_426dupAATAAT | 1.0 |
Pf3D7_13_v3 | 1727145 | PF3D7_1343700 | K13 | c.-148C>A | 1.0 |
Pf3D7_14_v3 | 1550187 | PF3D7_1438400 | MCA2 | c.174T>G | 0.97 |
Pf3D7_14_v3 | 1550518 | PF3D7_1438400 | MCA2 | p.ValAsnAsnMet169MetAsnAsnVal | 0.42 |
Pf3D7_14_v3 | 1550518 | PF3D7_1438400 | MCA2 | c.514_522delATGAATAAT | 0.58 |
Pf3D7_14_v3 | 1550893 | PF3D7_1438400 | MCA2 | c.904_906delAAT | 0.93 |
Pf3D7_14_v3 | 1550934 | PF3D7_1438400 | MCA2 | c.921T>C | 0.69 |
Pf3D7_14_v3 | 1550938 | PF3D7_1438400 | MCA2 | p.Val309Ile | 0.6 |
Pf3D7_14_v3 | 1550959 | PF3D7_1438400 | MCA2 | c.960_962delTAA | 1.0 |
Pf3D7_14_v3 | 1553266 | PF3D7_1438400 | MCA2 | p.Asn1085Asp | 1.0 |
Pf3D7_14_v3 | 1553697 | PF3D7_1438400 | MCA2 | c.3684C>T | 0.96 |
Chromosome | Position | Depth | Annotation |
---|---|---|---|
Pf3D7_07_v3 | 404407 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 404408 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 404409 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 405361 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 405362 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 405363 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_13_v3 | 1724975 | 7 | Type: drug_resistance, Drug: artemisinin, Source: https://www.who.int/publications/i/item/9789240012813 |
Chromosome: | Genome Position | Locus Tag | Gene Name | Change | Estimated fraction |
---|---|---|---|---|---|
Pf3D7_01_v3 | 190862 | PF3D7_0104300 | UBP1 | c.615_626delTAATAATAATAA | 1.0 |
Pf3D7_01_v3 | 190968 | PF3D7_0104300 | UBP1 | p.Tyr234Asn | 0.13 |
Pf3D7_01_v3 | 191198 | PF3D7_0104300 | UBP1 | c.941dupA | 0.18 |
Pf3D7_01_v3 | 191283 | PF3D7_0104300 | UBP1 | p.Asn339Asp | 0.38 |
Pf3D7_01_v3 | 191606 | PF3D7_0104300 | UBP1 | c.1338G>A | 0.25 |
Pf3D7_01_v3 | 192560 | PF3D7_0104300 | UBP1 | p.Lys764Asn | 0.38 |
Pf3D7_01_v3 | 192563 | PF3D7_0104300 | UBP1 | c.2295G>A | 0.35 |
Pf3D7_01_v3 | 192660 | PF3D7_0104300 | UBP1 | c.2403_2411delTGATGATGA | 1.0 |
Pf3D7_01_v3 | 194135 | PF3D7_0104300 | UBP1 | c.3880delA | 0.43 |
Pf3D7_01_v3 | 194284 | PF3D7_0104300 | UBP1 | c.4028delA | 0.17 |
Pf3D7_01_v3 | 194393 | PF3D7_0104300 | UBP1 | c.4139delA | 0.38 |
Pf3D7_01_v3 | 194843 | PF3D7_0104300 | UBP1 | p.Glu1528Asp | 0.33 |
Pf3D7_01_v3 | 194843 | PF3D7_0104300 | UBP1 | p.Glu1528Asp | 0.33 |
Pf3D7_01_v3 | 197265 | PF3D7_0104300 | UBP1 | p.Phe2333Leu | 0.91 |
Pf3D7_01_v3 | 199741 | PF3D7_0104300 | UBP1 | c.9240C>T | 0.2 |
Pf3D7_01_v3 | 199749 | PF3D7_0104300 | UBP1 | p.His3083Arg | 0.3 |
Pf3D7_04_v3 | 748054 | PF3D7_0417200 | DHFR-TS | c.-34T>A | 0.27 |
Pf3D7_05_v3 | 410638 | PF3D7_0509800 | PI4K | p.Gly124Asp | 1.0 |
Pf3D7_05_v3 | 410695 | PF3D7_0509800 | PI4K | p.Gly143Asp | 1.0 |
Pf3D7_05_v3 | 410704 | PF3D7_0509800 | PI4K | p.Asp146Gly | 1.0 |
Pf3D7_05_v3 | 410707 | PF3D7_0509800 | PI4K | p.Gly147Asp | 1.0 |
Pf3D7_05_v3 | 411123 | PF3D7_0509800 | PI4K | p.Asn286Asp | 0.14 |
Pf3D7_05_v3 | 411130 | PF3D7_0509800 | PI4K | p.Asn288Ser | 0.4 |
Pf3D7_05_v3 | 412910 | PF3D7_0509800 | PI4K | c.2646_2651delCAACAA | 0.5 |
Pf3D7_05_v3 | 413117 | PF3D7_0509800 | PI4K | c.2861delA | 0.13 |
Pf3D7_05_v3 | 413436 | PF3D7_0509800 | PI4K | p.Asp1057Tyr | 0.18 |
Pf3D7_05_v3 | 415296 | PF3D7_0509800 | PI4K | c.4668T>C | 1.0 |
Pf3D7_05_v3 | 957706 | PF3D7_0523000 | MDR1 | c.-183_-180delTATA | 1.0 |
Pf3D7_05_v3 | 959834 | PF3D7_0523000 | MDR1 | p.Asn649Asp | 0.39 |
Pf3D7_07_v3 | 404407 | PF3D7_0709000 | CRT | p.Ala220Ser | 1.0 |
Pf3D7_07_v3 | 405362 | PF3D7_0709000 | CRT | p.Asn326Ser | 1.0 |
Pf3D7_08_v3 | 548068 | PF3D7_0810800 | PPPK-DHPS | c.-131_-130delAT | 1.0 |
Pf3D7_08_v3 | 643630 | PF3D7_0813000 | PF3D7_0813000 | p.Asn419Ser | 0.19 |
Pf3D7_08_v3 | 643671 | PF3D7_0813000 | PF3D7_0813000 | c.1215C>T | 0.29 |
Pf3D7_08_v3 | 643675 | PF3D7_0813000 | PF3D7_0813000 | p.Ser404Asn | 0.21 |
Pf3D7_08_v3 | 643680 | PF3D7_0813000 | PF3D7_0813000 | c.1206T>C | 0.19 |
Pf3D7_08_v3 | 644336 | PF3D7_0813000 | PF3D7_0813000 | c.538_549delAGAGATAGAACA | 1.0 |
Pf3D7_10_v3 | 1047084 | PF3D7_1025000 | PF3D7_1025000 | p.Asn566Asp | 0.38 |
Pf3D7_10_v3 | 1047087 | PF3D7_1025000 | PF3D7_1025000 | p.Asn565Asp | 0.29 |
Pf3D7_10_v3 | 1047095 | PF3D7_1025000 | PF3D7_1025000 | c.1682_1684dupATA | 1.0 |
Pf3D7_10_v3 | 1047391 | PF3D7_1025000 | PF3D7_1025000 | c.1383_1388delAGATAA | 0.35 |
Pf3D7_10_v3 | 1047391 | PF3D7_1025000 | PF3D7_1025000 | c.1383_1388delAGATAA | 0.35 |
Pf3D7_10_v3 | 1049827 | PF3D7_1025000 | PF3D7_1025000 | c.-67G>A | 0.17 |
Pf3D7_10_v3 | 1450480 | PF3D7_1036800 | PF3D7_1036800 | p.Ser181Phe | 0.5 |
Pf3D7_10_v3 | 1451781 | PF3D7_1036800 | PF3D7_1036800 | c.-136delT | 0.4 |
Pf3D7_11_v3 | 1526429 | PF3D7_1138700 | PF3D7_1138700 | p.Ser1613Asn | 0.17 |
Pf3D7_11_v3 | 1529377 | PF3D7_1138700 | PF3D7_1138700 | c.1890C>T | 0.16 |
Pf3D7_12_v3 | 717853 | PF3D7_1218300 | AP2-MU | c.-102_-101insT | 1.0 |
Pf3D7_12_v3 | 717865 | PF3D7_1218300 | AP2-MU | c.-90_-89insTATATT | 1.0 |
Pf3D7_12_v3 | 1925560 | PF3D7_1246300 | PF3D7_1246300 | c.-81_-80delTA | 1.0 |
Pf3D7_12_v3 | 2091905 | PF3D7_1251200 | PF3D7_1251200 | c.-182_-181insTATA | 1.0 |
Pf3D7_12_v3 | 2094061 | PF3D7_1251200 | PF3D7_1251200 | c.1657_1659delAAT | 0.16 |
Pf3D7_13_v3 | 748998 | PF3D7_1318100 | PF3D7_1318100 | c.-28delA | 0.25 |
Pf3D7_13_v3 | 848114 | PF3D7_1320600 | RAB11a | p.Gln181Lys | 0.3 |
Pf3D7_13_v3 | 1727052 | PF3D7_1343700 | K13 | c.-55A>T | 1.0 |
Pf3D7_13_v3 | 1727056 | PF3D7_1343700 | K13 | c.-59A>T | 1.0 |
Pf3D7_13_v3 | 1727073 | PF3D7_1343700 | K13 | c.-76T>A | 1.0 |
Pf3D7_13_v3 | 1727101 | PF3D7_1343700 | K13 | c.-104A>T | 1.0 |
Pf3D7_14_v3 | 1548826 | PF3D7_1438400 | MCA2 | c.-91_-89delAAA | 0.4 |
Pf3D7_14_v3 | 1548826 | PF3D7_1438400 | MCA2 | c.-92G>A | 0.6 |
Pf3D7_14_v3 | 1548826 | PF3D7_1438400 | MCA2 | c.-91_-89delAAA | 0.4 |
Pf3D7_14_v3 | 1548826 | PF3D7_1438400 | MCA2 | c.-92G>A | 0.6 |
Pf3D7_14_v3 | 1550927 | PF3D7_1438400 | MCA2 | p.Ser305Asn | 0.21 |
Pf3D7_14_v3 | 1550945 | PF3D7_1438400 | MCA2 | p.Ser311Asn | 0.31 |
Pf3D7_14_v3 | 1552502 | PF3D7_1438400 | MCA2 | c.2501delA | 0.19 |
Pf3D7_14_v3 | 1556519 | PF3D7_1438400 | MCA2 | c.6000T>C | 1.0 |
Pf3D7_14_v3 | 2481070 | PF3D7_1460900 | ARPS10 | p.Val127Met | 1.0 |
Pf3D7_14_v3 | 2481073 | PF3D7_1460900 | ARPS10 | p.Asp128His | 1.0 |
Resistance variants report
Gene | Mutations |
---|---|
DHFR-TS |
p.Asn51Ile
p.Cys59Arg
p.Ser108Asn
p.Ile164Leu
|
MDR1 |
p.Tyr184Phe
|
CRT |
p.Lys76Thr
p.Gln271Glu
p.Ile356Thr
p.Arg371Ile
|
PPPK-DHPS |
p.Ser436Ala
p.Ala437Gly
|
Other variants
Gene | ([{'chrom': 'Pf3D7_01_v3', 'pos': 190143, 'ref': 'C', 'alt': 'CAT', 'depth': 17, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'upstream_gene_variant', 'change': 'c.-126_-125insAT', 'nucleotide_change': 'c.-126_-125insAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-126_-125insAT', 'protein_change': '', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 190260, 'ref': 'G', 'alt': 'A', 'depth': 25, 'freq': 0.96, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'upstream_gene_variant', 'change': 'c.-9G>A', 'nucleotide_change': 'c.-9G>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-9G>A', 'protein_change': '', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 190616, 'ref': 'A', 'alt': 'G', 'depth': 25, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 19, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'change': 'c.348A>G', 'nucleotide_change': 'c.348A>G', 'protein_change': 'p.Thr116Thr', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'nucleotide_change': 'c.348A>G', 'protein_change': 'p.Thr116Thr', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 191282, 'ref': 'C', 'alt': 'T', 'depth': 29, 'freq': 0.41, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'change': 'c.1014C>T', 'nucleotide_change': 'c.1014C>T', 'protein_change': 'p.Asp338Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1014C>T', 'protein_change': 'p.Asp338Asp', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 191685, 'ref': 'TATA', 'alt': 'T', 'depth': 20, 'freq': 0.95, 'sv': False, 'filter': 'pass', 'forward_reads': 9, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'conservative_inframe_deletion', 'change': 'c.1444_1446delAAT', 'nucleotide_change': 'c.1444_1446delAAT', 'protein_change': 'p.Asn482del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'conservative_inframe_deletion', 'nucleotide_change': 'c.1444_1446delAAT', 'protein_change': 'p.Asn482del', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 192111, 'ref': 'T', 'alt': 'C', 'depth': 44, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 21, 'reverse_reads': 23, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Tyr615His', 'nucleotide_change': 'c.1843T>C', 'protein_change': 'p.Tyr615His', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.1843T>C', 'protein_change': 'p.Tyr615His', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 192633, 'ref': 'A', 'alt': 'G', 'depth': 23, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 13, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Asn789Asp', 'nucleotide_change': 'c.2365A>G', 'protein_change': 'p.Asn789Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.2365A>G', 'protein_change': 'p.Asn789Asp', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 193167, 'ref': 'A', 'alt': 'G', 'depth': 23, 'freq': 0.96, 'sv': False, 'filter': 'pass', 'forward_reads': 7, 'reverse_reads': 15, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Met967Val', 'nucleotide_change': 'c.2899A>G', 'protein_change': 'p.Met967Val', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.2899A>G', 'protein_change': 'p.Met967Val', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 193299, 'ref': 'G', 'alt': 'A', 'depth': 30, 'freq': 0.97, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Glu1011Lys', 'nucleotide_change': 'c.3031G>A', 'protein_change': 'p.Glu1011Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.3031G>A', 'protein_change': 'p.Glu1011Lys', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 193667, 'ref': 'G', 'alt': 'C', 'depth': 28, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Arg1133Ser', 'nucleotide_change': 'c.3399G>C', 'protein_change': 'p.Arg1133Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.3399G>C', 'protein_change': 'p.Arg1133Ser', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 194117, 'ref': 'T', 'alt': 'C', 'depth': 21, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 17, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'change': 'c.3849T>C', 'nucleotide_change': 'c.3849T>C', 'protein_change': 'p.Phe1283Phe', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'nucleotide_change': 'c.3849T>C', 'protein_change': 'p.Phe1283Phe', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 194843, 'ref': 'CAAATATGAA', 'alt': 'C', 'depth': 15, 'freq': 0.67, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'change': 'c.4593_4601delAAAATATGA', 'nucleotide_change': 'c.4593_4601delAAAATATGA', 'protein_change': 'p.Glu1531_Tyr1533del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.4593_4601delAAAATATGA', 'protein_change': 'p.Glu1531_Tyr1533del', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 194843, 'ref': 'CAAATATGAA', 'alt': 'C', 'depth': 15, 'freq': 0.67, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'change': 'c.4593_4601delAAAATATGA', 'nucleotide_change': 'c.4593_4601delAAAATATGA', 'protein_change': 'p.Glu1531_Tyr1533del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.4593_4601delAAAATATGA', 'protein_change': 'p.Glu1531_Tyr1533del', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 196010, 'ref': 'A', 'alt': 'C', 'depth': 27, 'freq': 0.78, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Lys1914Asn', 'nucleotide_change': 'c.5742A>C', 'protein_change': 'p.Lys1914Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.5742A>C', 'protein_change': 'p.Lys1914Asn', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 196011, 'ref': 'G', 'alt': 'A', 'depth': 26, 'freq': 0.77, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Glu1915Lys', 'nucleotide_change': 'c.5743G>A', 'protein_change': 'p.Glu1915Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.5743G>A', 'protein_change': 'p.Glu1915Lys', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 196981, 'ref': 'G', 'alt': 'A', 'depth': 18, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 12, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Arg2238Lys', 'nucleotide_change': 'c.6713G>A', 'protein_change': 'p.Arg2238Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.6713G>A', 'protein_change': 'p.Arg2238Lys', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 201154, 'ref': 'T', 'alt': 'C', 'depth': 25, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 19, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Leu3475Ser', 'nucleotide_change': 'c.10424T>C', 'protein_change': 'p.Leu3475Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.10424T>C', 'protein_change': 'p.Leu3475Ser', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_03_v3', 'pos': 922867, 'ref': 'CAT', 'alt': 'C', 'depth': 20, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 14, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'upstream_gene_variant', 'change': 'c.-106_-105delAT', 'nucleotide_change': 'c.-106_-105delAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-106_-105delAT', 'protein_change': '', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_03_v3', 'pos': 924907, 'ref': 'G', 'alt': 'T', 'depth': 31, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 14, 'reverse_reads': 17, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'synonymous_variant', 'change': 'c.1806G>T', 'nucleotide_change': 'c.1806G>T', 'protein_change': 'p.Ser602Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1806G>T', 'protein_change': 'p.Ser602Ser', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_03_v3', 'pos': 925808, 'ref': 'A', 'alt': 'G', 'depth': 44, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 24, 'reverse_reads': 20, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'missense_variant', 'change': 'p.Lys903Glu', 'nucleotide_change': 'c.2707A>G', 'protein_change': 'p.Lys903Glu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'missense_variant', 'nucleotide_change': 'c.2707A>G', 'protein_change': 'p.Lys903Glu', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_03_v3', 'pos': 925890, 'ref': 'TTAATAA', 'alt': 'T', 'depth': 32, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 19, 'reverse_reads': 13, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'disruptive_inframe_deletion', 'change': 'c.2804_2809delATAATA', 'nucleotide_change': 'c.2804_2809delATAATA', 'protein_change': 'p.Asn935_Asn936del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.2804_2809delATAATA', 'protein_change': 'p.Asn935_Asn936del', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_03_v3', 'pos': 925967, 'ref': 'G', 'alt': 'A', 'depth': 30, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 22, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'missense_variant', 'change': 'p.Glu956Lys', 'nucleotide_change': 'c.2866G>A', 'protein_change': 'p.Glu956Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'missense_variant', 'nucleotide_change': 'c.2866G>A', 'protein_change': 'p.Glu956Lys', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_05_v3', 'pos': 410184, 'ref': 'C', 'alt': 'A', 'depth': 13, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 9, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'upstream_gene_variant', 'change': 'c.-84C>A', 'nucleotide_change': 'c.-84C>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-84C>A', 'protein_change': '', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 410338, 'ref': 'A', 'alt': 'T', 'depth': 28, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'change': 'p.His24Leu', 'nucleotide_change': 'c.71A>T', 'protein_change': 'p.His24Leu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'nucleotide_change': 'c.71A>T', 'protein_change': 'p.His24Leu', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 410566, 'ref': 'T', 'alt': 'C', 'depth': 25, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 19, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'change': 'p.Val100Ala', 'nucleotide_change': 'c.299T>C', 'protein_change': 'p.Val100Ala', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'nucleotide_change': 'c.299T>C', 'protein_change': 'p.Val100Ala', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 412910, 'ref': 'CAACAAC', 'alt': 'CAATAAT', 'depth': 14, 'freq': 0.5, 'sv': False, 'filter': 'pass', 'forward_reads': 3, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'change': 'c.2646_2649delCAACinsTAAT', 'nucleotide_change': 'c.2646_2649delCAACinsTAAT', 'protein_change': 'p.884', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.2646_2649delCAACinsTAAT', 'protein_change': 'p.884', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 413414, 'ref': 'T', 'alt': 'C', 'depth': 16, 'freq': 0.56, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'change': 'c.3147T>C', 'nucleotide_change': 'c.3147T>C', 'protein_change': 'p.Asp1049Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.3147T>C', 'protein_change': 'p.Asp1049Asp', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 959840, 'ref': 'G', 'alt': 'A', 'depth': 30, 'freq': 0.43, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 5, 'sv_len': None, 'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'missense_variant', 'change': 'p.Asp651Asn', 'nucleotide_change': 'c.1951G>A', 'protein_change': 'p.Asp651Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'missense_variant', 'nucleotide_change': 'c.1951G>A', 'protein_change': 'p.Asp651Asn', 'annotation': [], 'gene': 'MDR1'}], 'gene': 'MDR1'}, {'chrom': 'Pf3D7_07_v3', 'pos': 403620, 'ref': 'GA', 'alt': 'TG', 'depth': 12, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0709000', 'feature_id': 'transcript:PF3D7_0709000', 'type': 'missense_variant', 'change': 'p.MetAsn74IleAsp', 'nucleotide_change': 'c.222_223delGAinsTG', 'protein_change': 'p.MetAsn74IleAsp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0709000', 'feature_id': 'transcript:PF3D7_0709000', 'type': 'missense_variant', 'nucleotide_change': 'c.222_223delGAinsTG', 'protein_change': 'p.MetAsn74IleAsp', 'annotation': [], 'gene': 'CRT'}], 'gene': 'CRT'}, {'chrom': 'Pf3D7_07_v3', 'pos': 403623, 'ref': 'T', 'alt': 'A', 'depth': 11, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 3, 'sv_len': None, 'gene_id': 'PF3D7_0709000', 'feature_id': 'transcript:PF3D7_0709000', 'type': 'missense_variant', 'change': 'p.Asn75Lys', 'nucleotide_change': 'c.225T>A', 'protein_change': 'p.Asn75Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0709000', 'feature_id': 'transcript:PF3D7_0709000', 'type': 'missense_variant', 'nucleotide_change': 'c.225T>A', 'protein_change': 'p.Asn75Lys', 'annotation': [], 'gene': 'CRT'}], 'gene': 'CRT'}, {'chrom': 'Pf3D7_08_v3', 'pos': 643648, 'ref': 'C', 'alt': 'T', 'depth': 39, 'freq': 0.49, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'missense_variant', 'change': 'p.Ser413Asn', 'nucleotide_change': 'c.1238G>A', 'protein_change': 'p.Ser413Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'missense_variant', 'nucleotide_change': 'c.1238G>A', 'protein_change': 'p.Ser413Asn', 'annotation': [], 'gene': 'PF3D7_0813000'}], 'gene': 'PF3D7_0813000'}, {'chrom': 'Pf3D7_08_v3', 'pos': 644936, 'ref': 'G', 'alt': 'T', 'depth': 15, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'upstream_gene_variant', 'change': 'c.-51C>A', 'nucleotide_change': 'c.-51C>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-51C>A', 'protein_change': '', 'annotation': [], 'gene': 'PF3D7_0813000'}], 'gene': 'PF3D7_0813000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1045876, 'ref': 'G', 'alt': 'C', 'depth': 12, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Gln932Glu', 'nucleotide_change': 'c.2794C>G', 'protein_change': 'p.Gln932Glu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.2794C>G', 'protein_change': 'p.Gln932Glu', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1046056, 'ref': 'G', 'alt': 'C', 'depth': 24, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 15, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'change': 'c.2724C>G', 'nucleotide_change': 'c.2724C>G', 'protein_change': 'p.Thr908Thr', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'nucleotide_change': 'c.2724C>G', 'protein_change': 'p.Thr908Thr', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047323, 'ref': 'A', 'alt': 'G', 'depth': 32, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 21, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Phe486Ser', 'nucleotide_change': 'c.1457T>C', 'protein_change': 'p.Phe486Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1457T>C', 'protein_change': 'p.Phe486Ser', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047391, 'ref': 'TTTATCT', 'alt': 'TTTATCC', 'depth': 20, 'freq': 0.65, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 3, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'change': 'c.1383A>G', 'nucleotide_change': 'c.1383A>G', 'protein_change': 'p.Lys461Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1383A>G', 'protein_change': 'p.Lys461Lys', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047391, 'ref': 'TTTATCT', 'alt': 'TTTATCC', 'depth': 20, 'freq': 0.65, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 3, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'change': 'c.1383A>G', 'nucleotide_change': 'c.1383A>G', 'protein_change': 'p.Lys461Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1383A>G', 'protein_change': 'p.Lys461Lys', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1049903, 'ref': 'AAT', 'alt': 'A', 'depth': 18, 'freq': 0.94, 'sv': False, 'filter': 'pass', 'forward_reads': 9, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'upstream_gene_variant', 'change': 'c.-145_-144delAT', 'nucleotide_change': 'c.-145_-144delAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-145_-144delAT', 'protein_change': '', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1449646, 'ref': 'G', 'alt': 'A', 'depth': 36, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 16, 'reverse_reads': 20, 'sv_len': None, 'gene_id': 'PF3D7_1036800', 'feature_id': 'transcript:PF3D7_1036800', 'type': 'missense_variant', 'change': 'p.Thr459Ile', 'nucleotide_change': 'c.1376C>T', 'protein_change': 'p.Thr459Ile', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1036800', 'feature_id': 'transcript:PF3D7_1036800', 'type': 'missense_variant', 'nucleotide_change': 'c.1376C>T', 'protein_change': 'p.Thr459Ile', 'annotation': [], 'gene': 'PF3D7_1036800'}], 'gene': 'PF3D7_1036800'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1526106, 'ref': 'A', 'alt': 'C', 'depth': 42, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 22, 'reverse_reads': 20, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'change': 'p.Ser1721Ala', 'nucleotide_change': 'c.5161T>G', 'protein_change': 'p.Ser1721Ala', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'nucleotide_change': 'c.5161T>G', 'protein_change': 'p.Ser1721Ala', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1529369, 'ref': 'C', 'alt': 'T', 'depth': 25, 'freq': 0.8, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 7, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'change': 'p.Ser633Asn', 'nucleotide_change': 'c.1898G>A', 'protein_change': 'p.Ser633Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'nucleotide_change': 'c.1898G>A', 'protein_change': 'p.Ser633Asn', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1529778, 'ref': 'C', 'alt': 'G', 'depth': 40, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 22, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'change': 'p.Glu497Gln', 'nucleotide_change': 'c.1489G>C', 'protein_change': 'p.Glu497Gln', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'nucleotide_change': 'c.1489G>C', 'protein_change': 'p.Glu497Gln', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1530261, 'ref': 'C', 'alt': 'G', 'depth': 36, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'change': 'p.Glu336Gln', 'nucleotide_change': 'c.1006G>C', 'protein_change': 'p.Glu336Gln', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'nucleotide_change': 'c.1006G>C', 'protein_change': 'p.Glu336Gln', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_12_v3', 'pos': 211053, 'ref': 'CAT', 'alt': 'C', 'depth': 19, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 14, 'sv_len': None, 'gene_id': 'PF3D7_1204400', 'feature_id': 'transcript:PF3D7_1204400', 'type': 'upstream_gene_variant', 'change': 'c.-162_-161delAT', 'nucleotide_change': 'c.-162_-161delAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1204400', 'feature_id': 'transcript:PF3D7_1204400', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-162_-161delAT', 'protein_change': '', 'annotation': [], 'gene': 'PF3D7_1204400'}], 'gene': 'PF3D7_1204400'}, {'chrom': 'Pf3D7_12_v3', 'pos': 529418, 'ref': 'C', 'alt': 'T', 'depth': 16, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'missense_variant', 'change': 'p.Gly1128Arg', 'nucleotide_change': 'c.3382G>A', 'protein_change': 'p.Gly1128Arg', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'missense_variant', 'nucleotide_change': 'c.3382G>A', 'protein_change': 'p.Gly1128Arg', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 532131, 'ref': 'G', 'alt': 'T', 'depth': 23, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'synonymous_variant', 'change': 'c.669C>A', 'nucleotide_change': 'c.669C>A', 'protein_change': 'p.Gly223Gly', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'synonymous_variant', 'nucleotide_change': 'c.669C>A', 'protein_change': 'p.Gly223Gly', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 532889, 'ref': 'GATATAGAT', 'alt': 'G', 'depth': 13, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 9, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'upstream_gene_variant', 'change': 'c.-98_-91delATCTATAT', 'nucleotide_change': 'c.-98_-91delATCTATAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-98_-91delATCTATAT', 'protein_change': '', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 591301, 'ref': 'T', 'alt': 'C', 'depth': 24, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'synonymous_variant', 'change': 'c.1134A>G', 'nucleotide_change': 'c.1134A>G', 'protein_change': 'p.Leu378Leu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1134A>G', 'protein_change': 'p.Leu378Leu', 'annotation': [], 'gene': 'PRS'}], 'gene': 'PRS'}, {'chrom': 'Pf3D7_12_v3', 'pos': 592329, 'ref': 'C', 'alt': 'T', 'depth': 39, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 21, 'sv_len': None, 'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'missense_variant', 'change': 'p.Val36Ile', 'nucleotide_change': 'c.106G>A', 'protein_change': 'p.Val36Ile', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'missense_variant', 'nucleotide_change': 'c.106G>A', 'protein_change': 'p.Val36Ile', 'annotation': [], 'gene': 'PRS'}], 'gene': 'PRS'}, {'chrom': 'Pf3D7_12_v3', 'pos': 592496, 'ref': 'C', 'alt': 'T', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'upstream_gene_variant', 'change': 'c.-62G>A', 'nucleotide_change': 'c.-62G>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-62G>A', 'protein_change': '', 'annotation': [], 'gene': 'PRS'}], 'gene': 'PRS'}, {'chrom': 'Pf3D7_12_v3', 'pos': 718631, 'ref': 'TTAA', 'alt': 'T', 'depth': 19, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_1218300', 'feature_id': 'transcript:PF3D7_1218300', 'type': 'disruptive_inframe_deletion', 'change': 'c.699_701delTAA', 'nucleotide_change': 'c.699_701delTAA', 'protein_change': 'p.Asn233del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1218300', 'feature_id': 'transcript:PF3D7_1218300', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.699_701delTAA', 'protein_change': 'p.Asn233del', 'annotation': [], 'gene': 'AP2-MU'}], 'gene': 'AP2-MU'}, {'chrom': 'Pf3D7_12_v3', 'pos': 1927229, 'ref': 'T', 'alt': 'C', 'depth': 28, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_1246300', 'feature_id': 'transcript:PF3D7_1246300', 'type': 'synonymous_variant', 'change': 'c.1041T>C', 'nucleotide_change': 'c.1041T>C', 'protein_change': 'p.Phe347Phe', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1246300', 'feature_id': 'transcript:PF3D7_1246300', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1041T>C', 'protein_change': 'p.Phe347Phe', 'annotation': [], 'gene': 'PF3D7_1246300'}], 'gene': 'PF3D7_1246300'}, {'chrom': 'Pf3D7_12_v3', 'pos': 2093058, 'ref': 'A', 'alt': 'G', 'depth': 27, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 16, 'sv_len': None, 'gene_id': 'PF3D7_1251200', 'feature_id': 'transcript:PF3D7_1251200', 'type': 'synonymous_variant', 'change': 'c.636A>G', 'nucleotide_change': 'c.636A>G', 'protein_change': 'p.Lys212Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1251200', 'feature_id': 'transcript:PF3D7_1251200', 'type': 'synonymous_variant', 'nucleotide_change': 'c.636A>G', 'protein_change': 'p.Lys212Lys', 'annotation': [], 'gene': 'PF3D7_1251200'}], 'gene': 'PF3D7_1251200'}, {'chrom': 'Pf3D7_13_v3', 'pos': 1726571, 'ref': 'G', 'alt': 'GATTATT', 'depth': 16, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 7, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'conservative_inframe_insertion', 'change': 'c.421_426dupAATAAT', 'nucleotide_change': 'c.421_426dupAATAAT', 'protein_change': 'p.Asn141_Asn142dup', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'conservative_inframe_insertion', 'nucleotide_change': 'c.421_426dupAATAAT', 'protein_change': 'p.Asn141_Asn142dup', 'annotation': [], 'gene': 'K13'}], 'gene': 'K13'}, {'chrom': 'Pf3D7_13_v3', 'pos': 1727145, 'ref': 'G', 'alt': 'T', 'depth': 17, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'change': 'c.-148C>A', 'nucleotide_change': 'c.-148C>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-148C>A', 'protein_change': '', 'annotation': [], 'gene': 'K13'}], 'gene': 'K13'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550187, 'ref': 'T', 'alt': 'G', 'depth': 36, 'freq': 0.97, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 15, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'change': 'c.174T>G', 'nucleotide_change': 'c.174T>G', 'protein_change': 'p.Ser58Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'nucleotide_change': 'c.174T>G', 'protein_change': 'p.Ser58Ser', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550518, 'ref': 'GTGAATAATA', 'alt': 'ATGAATAATG', 'depth': 19, 'freq': 0.42, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.ValAsnAsnMet169MetAsnAsnVal', 'nucleotide_change': 'c.505_514delGTGAATAATAinsATGAATAATG', 'protein_change': 'p.ValAsnAsnMet169MetAsnAsnVal', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.505_514delGTGAATAATAinsATGAATAATG', 'protein_change': 'p.ValAsnAsnMet169MetAsnAsnVal', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550518, 'ref': 'GTGAATAATA', 'alt': 'G', 'depth': 19, 'freq': 0.58, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 7, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'conservative_inframe_deletion', 'change': 'c.514_522delATGAATAAT', 'nucleotide_change': 'c.514_522delATGAATAAT', 'protein_change': 'p.Met172_Asn174del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'conservative_inframe_deletion', 'nucleotide_change': 'c.514_522delATGAATAAT', 'protein_change': 'p.Met172_Asn174del', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550893, 'ref': 'TATA', 'alt': 'T', 'depth': 14, 'freq': 0.93, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'conservative_inframe_deletion', 'change': 'c.904_906delAAT', 'nucleotide_change': 'c.904_906delAAT', 'protein_change': 'p.Asn302del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'conservative_inframe_deletion', 'nucleotide_change': 'c.904_906delAAT', 'protein_change': 'p.Asn302del', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550934, 'ref': 'T', 'alt': 'C', 'depth': 16, 'freq': 0.69, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 7, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'change': 'c.921T>C', 'nucleotide_change': 'c.921T>C', 'protein_change': 'p.Asn307Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'nucleotide_change': 'c.921T>C', 'protein_change': 'p.Asn307Asn', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550938, 'ref': 'G', 'alt': 'A', 'depth': 15, 'freq': 0.6, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 5, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.Val309Ile', 'nucleotide_change': 'c.925G>A', 'protein_change': 'p.Val309Ile', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.925G>A', 'protein_change': 'p.Val309Ile', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550959, 'ref': 'TATA', 'alt': 'T', 'depth': 14, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 3, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'disruptive_inframe_deletion', 'change': 'c.960_962delTAA', 'nucleotide_change': 'c.960_962delTAA', 'protein_change': 'p.Asn321del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.960_962delTAA', 'protein_change': 'p.Asn321del', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1553266, 'ref': 'A', 'alt': 'G', 'depth': 38, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 15, 'reverse_reads': 23, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.Asn1085Asp', 'nucleotide_change': 'c.3253A>G', 'protein_change': 'p.Asn1085Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.3253A>G', 'protein_change': 'p.Asn1085Asp', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1553697, 'ref': 'C', 'alt': 'T', 'depth': 24, 'freq': 0.96, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'change': 'c.3684C>T', 'nucleotide_change': 'c.3684C>T', 'protein_change': 'p.His1228His', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'nucleotide_change': 'c.3684C>T', 'protein_change': 'p.His1228His', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}], {'chrom': 'Chromosome:', 'pos': 'Genome Position', 'gene_id': 'Locus Tag', 'gene': 'Gene Name', 'change': 'Change', 'freq': 'Estimated fraction'}, 'Other variants', 'falciparum')Mutations |
---|---|
UBP1 |
c.-126_-125insAT
c.-9G>A
c.348A>G
c.1014C>T
c.1444_1446delAAT
p.Tyr615His
p.Asn789Asp
p.Met967Val
p.Glu1011Lys
p.Arg1133Ser
c.3849T>C
c.4593_4601delAAAATATGA
c.4593_4601delAAAATATGA
p.Lys1914Asn
p.Glu1915Lys
p.Arg2238Lys
p.Leu3475Ser
|
CARL |
c.-106_-105delAT
c.1806G>T
p.Lys903Glu
c.2804_2809delATAATA
p.Glu956Lys
|
PI4K |
c.-84C>A
p.His24Leu
p.Val100Ala
c.2646_2649delCAACinsTAAT
c.3147T>C
|
MDR1 |
p.Asp651Asn
|
CRT |
p.MetAsn74IleAsp
p.Asn75Lys
|
PF3D7_0813000 |
p.Ser413Asn
c.-51C>A
|
PF3D7_1025000 |
p.Gln932Glu
c.2724C>G
p.Phe486Ser
c.1383A>G
c.1383A>G
c.-145_-144delAT
|
PF3D7_1036800 |
p.Thr459Ile
|
PF3D7_1138700 |
p.Ser1721Ala
p.Ser633Asn
p.Glu497Gln
p.Glu336Gln
|
PF3D7_1204400 |
c.-162_-161delAT
|
ATP4 |
p.Gly1128Arg
c.669C>A
c.-98_-91delATCTATAT
|
PRS |
c.1134A>G
p.Val36Ile
c.-62G>A
|
AP2-MU |
c.699_701delTAA
|
PF3D7_1246300 |
c.1041T>C
|
PF3D7_1251200 |
c.636A>G
|
K13 |
c.421_426dupAATAAT
c.-148C>A
|
MCA2 |
c.174T>G
p.ValAsnAsnMet169MetAsnAsnVal
c.514_522delATGAATAAT
c.904_906delAAT
c.921T>C
p.Val309Ile
c.960_962delTAA
p.Asn1085Asp
c.3684C>T
|
QC failed variants
Gene | Mutations |
---|---|
UBP1 |
|
DHFR-TS |
|
PI4K |
|
MDR1 |
|
CRT |
|
PPPK-DHPS |
|
PF3D7_0813000 |
|
PF3D7_1025000 |
|
PF3D7_1036800 |
|
PF3D7_1138700 |
|
AP2-MU |
|
PF3D7_1246300 |
|
PF3D7_1251200 |
|
PF3D7_1318100 |
|
RAB11a |
|
K13 |
|
MCA2 |
|
ARPS10 |
|
Missing positions report
Gene | Mutations |
---|---|
|
Southeast Asia - 90.0%
Percentage of barcoding SNPs that have coverage: 0 %
Process | Software |
---|---|
Trimming | Trimmomatic |
Mapping | Bwa |
Variant_calling | Freebayes |
Depth_calculation | Samtools |
This section shows the average number of reads that align to, or 'cover', known reference bases
NextGene | Percentage Depth passed | Median Depth |
---|---|---|
UBP1 | 96.43 | 29.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_0109800 | 95.25 | 29.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
CARL | 87.69 | 25.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
DHFR-TS | 95.76 | 28.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PI4K | 89.4 | 26.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
MDR1 | 99.64 | 34.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
DHODH | 89.72 | 33.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
CRT | 73.57 | 15.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PPPK-DHPS | 95.95 | 28.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_0813000 | 89.55 | 25.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_1025000 | 84.52 | 26.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_1036800 | 88.7 | 22.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_1113300 | 91.13 | 28.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_1138700 | 94.08 | 33.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_1204400 | 81.82 | 19.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
ATP4 | 99.64 | 29.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PRS | 97.05 | 31.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
AP2-MU | 92.41 | 29.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_1246300 | 83.49 | 18.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_1251200 | 87.03 | 26.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
PF3D7_1318100 | 97.26 | 24.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
RAB11a | 84.42 | 17.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
K13 | 97.23 | 30.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
MCA2 | 96.75 | 30.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
eEF2 | 95.9 | 23.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
ARPS10 | 73.95 | 13.0 |
Gene | Percentage Depth passed | Median Depth |
---|---|---|
CYTB | 100.0 | 385.0 |
Gene | Percentage depth passed | Median Depth |
---|---|---|
UBP1 | 96.43 | 29.0 |
PF3D7_0109800 | 95.25 | 29.0 |
CARL | 87.69 | 25.0 |
DHFR-TS | 95.76 | 28.0 |
PI4K | 89.4 | 26.0 |
MDR1 | 99.64 | 34.0 |
DHODH | 89.72 | 33.0 |
CRT | 73.57 | 15.0 |
PPPK-DHPS | 95.95 | 28.0 |
PF3D7_0813000 | 89.55 | 25.0 |
PF3D7_1025000 | 84.52 | 26.0 |
PF3D7_1036800 | 88.7 | 22.0 |
PF3D7_1113300 | 91.13 | 28.0 |
PF3D7_1138700 | 94.08 | 33.0 |
PF3D7_1204400 | 81.82 | 19.0 |
ATP4 | 99.64 | 29.0 |
PRS | 97.05 | 31.0 |
AP2-MU | 92.41 | 29.0 |
PF3D7_1246300 | 83.49 | 18.0 |
PF3D7_1251200 | 87.03 | 26.0 |
PF3D7_1318100 | 97.26 | 24.0 |
RAB11a | 84.42 | 17.0 |
K13 | 97.23 | 30.0 |
MCA2 | 96.75 | 30.0 |
eEF2 | 95.9 | 23.0 |
ARPS10 | 73.95 | 13.0 |
CYTB | 100.0 | 385.0 |
Identifier | Date |
---|---|
Cefa3f2e-D334-4fa5-91ac-920f39cc11a0 | Sun Sep 8 02:32:45 2024 |
Plasmodium falciparum
Species | Prediction |
---|---|
Plasmodium falciparum |
99.76 |
Drug | Mutations |
---|---|
Chloroquine |
MDR1 p.Tyr184Phe (1.00) , CRT p.Lys76Thr (1.00) , CRT p.Gln271Glu (1.00) , CRT p.Ile356Thr (1.00) , CRT p.Arg371Ile (1.00) |
Mefloquine |
|
Pyrimethamine |
DHFR-TS p.Asn51Ile (1.00) , DHFR-TS p.Cys59Arg (1.00) , DHFR-TS p.Ser108Asn (1.00) , DHFR-TS p.Ile164Leu (1.00) |
Sulfadoxine |
PPPK-DHPS p.Ser436Ala (1.00) , PPPK-DHPS p.Ala437Gly (1.00) |
Artemisinin |
Chromosome: | Genome Position | Locus Tag | Gene Name | Change | Estimated fraction |
---|---|---|---|---|---|
Pf3D7_01_v3 | 190143 | PF3D7_0104300 | UBP1 | c.-126_-125insAT | 1.0 |
Pf3D7_01_v3 | 190260 | PF3D7_0104300 | UBP1 | c.-9G>A | 0.96 |
Pf3D7_01_v3 | 190616 | PF3D7_0104300 | UBP1 | c.348A>G | 1.0 |
Pf3D7_01_v3 | 191282 | PF3D7_0104300 | UBP1 | c.1014C>T | 0.41 |
Pf3D7_01_v3 | 191685 | PF3D7_0104300 | UBP1 | c.1444_1446delAAT | 0.95 |
Pf3D7_01_v3 | 192111 | PF3D7_0104300 | UBP1 | p.Tyr615His | 1.0 |
Pf3D7_01_v3 | 192633 | PF3D7_0104300 | UBP1 | p.Asn789Asp | 1.0 |
Pf3D7_01_v3 | 193167 | PF3D7_0104300 | UBP1 | p.Met967Val | 0.96 |
Pf3D7_01_v3 | 193299 | PF3D7_0104300 | UBP1 | p.Glu1011Lys | 0.97 |
Pf3D7_01_v3 | 193667 | PF3D7_0104300 | UBP1 | p.Arg1133Ser | 1.0 |
Pf3D7_01_v3 | 194117 | PF3D7_0104300 | UBP1 | c.3849T>C | 1.0 |
Pf3D7_01_v3 | 194843 | PF3D7_0104300 | UBP1 | c.4593_4601delAAAATATGA | 0.67 |
Pf3D7_01_v3 | 194843 | PF3D7_0104300 | UBP1 | c.4593_4601delAAAATATGA | 0.67 |
Pf3D7_01_v3 | 196010 | PF3D7_0104300 | UBP1 | p.Lys1914Asn | 0.78 |
Pf3D7_01_v3 | 196011 | PF3D7_0104300 | UBP1 | p.Glu1915Lys | 0.77 |
Pf3D7_01_v3 | 196981 | PF3D7_0104300 | UBP1 | p.Arg2238Lys | 1.0 |
Pf3D7_01_v3 | 201154 | PF3D7_0104300 | UBP1 | p.Leu3475Ser | 1.0 |
Pf3D7_03_v3 | 922867 | PF3D7_0321900 | CARL | c.-106_-105delAT | 1.0 |
Pf3D7_03_v3 | 924907 | PF3D7_0321900 | CARL | c.1806G>T | 1.0 |
Pf3D7_03_v3 | 925808 | PF3D7_0321900 | CARL | p.Lys903Glu | 1.0 |
Pf3D7_03_v3 | 925890 | PF3D7_0321900 | CARL | c.2804_2809delATAATA | 1.0 |
Pf3D7_03_v3 | 925967 | PF3D7_0321900 | CARL | p.Glu956Lys | 1.0 |
Pf3D7_05_v3 | 410184 | PF3D7_0509800 | PI4K | c.-84C>A | 1.0 |
Pf3D7_05_v3 | 410338 | PF3D7_0509800 | PI4K | p.His24Leu | 1.0 |
Pf3D7_05_v3 | 410566 | PF3D7_0509800 | PI4K | p.Val100Ala | 1.0 |
Pf3D7_05_v3 | 412910 | PF3D7_0509800 | PI4K | c.2646_2649delCAACinsTAAT | 0.5 |
Pf3D7_05_v3 | 413414 | PF3D7_0509800 | PI4K | c.3147T>C | 0.56 |
Pf3D7_05_v3 | 959840 | PF3D7_0523000 | MDR1 | p.Asp651Asn | 0.43 |
Pf3D7_07_v3 | 403620 | PF3D7_0709000 | CRT | p.MetAsn74IleAsp | 1.0 |
Pf3D7_07_v3 | 403623 | PF3D7_0709000 | CRT | p.Asn75Lys | 1.0 |
Pf3D7_08_v3 | 643648 | PF3D7_0813000 | PF3D7_0813000 | p.Ser413Asn | 0.49 |
Pf3D7_08_v3 | 644936 | PF3D7_0813000 | PF3D7_0813000 | c.-51C>A | 1.0 |
Pf3D7_10_v3 | 1045876 | PF3D7_1025000 | PF3D7_1025000 | p.Gln932Glu | 1.0 |
Pf3D7_10_v3 | 1046056 | PF3D7_1025000 | PF3D7_1025000 | c.2724C>G | 1.0 |
Pf3D7_10_v3 | 1047323 | PF3D7_1025000 | PF3D7_1025000 | p.Phe486Ser | 1.0 |
Pf3D7_10_v3 | 1047391 | PF3D7_1025000 | PF3D7_1025000 | c.1383A>G | 0.65 |
Pf3D7_10_v3 | 1047391 | PF3D7_1025000 | PF3D7_1025000 | c.1383A>G | 0.65 |
Pf3D7_10_v3 | 1049903 | PF3D7_1025000 | PF3D7_1025000 | c.-145_-144delAT | 0.94 |
Pf3D7_10_v3 | 1449646 | PF3D7_1036800 | PF3D7_1036800 | p.Thr459Ile | 1.0 |
Pf3D7_11_v3 | 1526106 | PF3D7_1138700 | PF3D7_1138700 | p.Ser1721Ala | 1.0 |
Pf3D7_11_v3 | 1529369 | PF3D7_1138700 | PF3D7_1138700 | p.Ser633Asn | 0.8 |
Pf3D7_11_v3 | 1529778 | PF3D7_1138700 | PF3D7_1138700 | p.Glu497Gln | 1.0 |
Pf3D7_11_v3 | 1530261 | PF3D7_1138700 | PF3D7_1138700 | p.Glu336Gln | 1.0 |
Pf3D7_12_v3 | 211053 | PF3D7_1204400 | PF3D7_1204400 | c.-162_-161delAT | 1.0 |
Pf3D7_12_v3 | 529418 | PF3D7_1211900 | ATP4 | p.Gly1128Arg | 1.0 |
Pf3D7_12_v3 | 532131 | PF3D7_1211900 | ATP4 | c.669C>A | 1.0 |
Pf3D7_12_v3 | 532889 | PF3D7_1211900 | ATP4 | c.-98_-91delATCTATAT | 1.0 |
Pf3D7_12_v3 | 591301 | PF3D7_1213800 | PRS | c.1134A>G | 1.0 |
Pf3D7_12_v3 | 592329 | PF3D7_1213800 | PRS | p.Val36Ile | 1.0 |
Pf3D7_12_v3 | 592496 | PF3D7_1213800 | PRS | c.-62G>A | 1.0 |
Pf3D7_12_v3 | 718631 | PF3D7_1218300 | AP2-MU | c.699_701delTAA | 1.0 |
Pf3D7_12_v3 | 1927229 | PF3D7_1246300 | PF3D7_1246300 | c.1041T>C | 1.0 |
Pf3D7_12_v3 | 2093058 | PF3D7_1251200 | PF3D7_1251200 | c.636A>G | 1.0 |
Pf3D7_13_v3 | 1726571 | PF3D7_1343700 | K13 | c.421_426dupAATAAT | 1.0 |
Pf3D7_13_v3 | 1727145 | PF3D7_1343700 | K13 | c.-148C>A | 1.0 |
Pf3D7_14_v3 | 1550187 | PF3D7_1438400 | MCA2 | c.174T>G | 0.97 |
Pf3D7_14_v3 | 1550518 | PF3D7_1438400 | MCA2 | p.ValAsnAsnMet169MetAsnAsnVal | 0.42 |
Pf3D7_14_v3 | 1550518 | PF3D7_1438400 | MCA2 | c.514_522delATGAATAAT | 0.58 |
Pf3D7_14_v3 | 1550893 | PF3D7_1438400 | MCA2 | c.904_906delAAT | 0.93 |
Pf3D7_14_v3 | 1550934 | PF3D7_1438400 | MCA2 | c.921T>C | 0.69 |
Pf3D7_14_v3 | 1550938 | PF3D7_1438400 | MCA2 | p.Val309Ile | 0.6 |
Pf3D7_14_v3 | 1550959 | PF3D7_1438400 | MCA2 | c.960_962delTAA | 1.0 |
Pf3D7_14_v3 | 1553266 | PF3D7_1438400 | MCA2 | p.Asn1085Asp | 1.0 |
Pf3D7_14_v3 | 1553697 | PF3D7_1438400 | MCA2 | c.3684C>T | 0.96 |
Chromosome: | Genome Position | Locus Tag | Gene Name | Change | Estimated fraction |
---|---|---|---|---|---|
Pf3D7_01_v3 | 190862 | PF3D7_0104300 | UBP1 | c.615_626delTAATAATAATAA | 1.0 |
Pf3D7_01_v3 | 190968 | PF3D7_0104300 | UBP1 | p.Tyr234Asn | 0.13 |
Pf3D7_01_v3 | 191198 | PF3D7_0104300 | UBP1 | c.941dupA | 0.18 |
Pf3D7_01_v3 | 191283 | PF3D7_0104300 | UBP1 | p.Asn339Asp | 0.38 |
Pf3D7_01_v3 | 191606 | PF3D7_0104300 | UBP1 | c.1338G>A | 0.25 |
Pf3D7_01_v3 | 192560 | PF3D7_0104300 | UBP1 | p.Lys764Asn | 0.38 |
Pf3D7_01_v3 | 192563 | PF3D7_0104300 | UBP1 | c.2295G>A | 0.35 |
Pf3D7_01_v3 | 192660 | PF3D7_0104300 | UBP1 | c.2403_2411delTGATGATGA | 1.0 |
Pf3D7_01_v3 | 194135 | PF3D7_0104300 | UBP1 | c.3880delA | 0.43 |
Pf3D7_01_v3 | 194284 | PF3D7_0104300 | UBP1 | c.4028delA | 0.17 |
Pf3D7_01_v3 | 194393 | PF3D7_0104300 | UBP1 | c.4139delA | 0.38 |
Pf3D7_01_v3 | 194843 | PF3D7_0104300 | UBP1 | p.Glu1528Asp | 0.33 |
Pf3D7_01_v3 | 194843 | PF3D7_0104300 | UBP1 | p.Glu1528Asp | 0.33 |
Pf3D7_01_v3 | 197265 | PF3D7_0104300 | UBP1 | p.Phe2333Leu | 0.91 |
Pf3D7_01_v3 | 199741 | PF3D7_0104300 | UBP1 | c.9240C>T | 0.2 |
Pf3D7_01_v3 | 199749 | PF3D7_0104300 | UBP1 | p.His3083Arg | 0.3 |
Pf3D7_04_v3 | 748054 | PF3D7_0417200 | DHFR-TS | c.-34T>A | 0.27 |
Pf3D7_05_v3 | 410638 | PF3D7_0509800 | PI4K | p.Gly124Asp | 1.0 |
Pf3D7_05_v3 | 410695 | PF3D7_0509800 | PI4K | p.Gly143Asp | 1.0 |
Pf3D7_05_v3 | 410704 | PF3D7_0509800 | PI4K | p.Asp146Gly | 1.0 |
Pf3D7_05_v3 | 410707 | PF3D7_0509800 | PI4K | p.Gly147Asp | 1.0 |
Pf3D7_05_v3 | 411123 | PF3D7_0509800 | PI4K | p.Asn286Asp | 0.14 |
Pf3D7_05_v3 | 411130 | PF3D7_0509800 | PI4K | p.Asn288Ser | 0.4 |
Pf3D7_05_v3 | 412910 | PF3D7_0509800 | PI4K | c.2646_2651delCAACAA | 0.5 |
Pf3D7_05_v3 | 413117 | PF3D7_0509800 | PI4K | c.2861delA | 0.13 |
Pf3D7_05_v3 | 413436 | PF3D7_0509800 | PI4K | p.Asp1057Tyr | 0.18 |
Pf3D7_05_v3 | 415296 | PF3D7_0509800 | PI4K | c.4668T>C | 1.0 |
Pf3D7_05_v3 | 957706 | PF3D7_0523000 | MDR1 | c.-183_-180delTATA | 1.0 |
Pf3D7_05_v3 | 959834 | PF3D7_0523000 | MDR1 | p.Asn649Asp | 0.39 |
Pf3D7_07_v3 | 404407 | PF3D7_0709000 | CRT | p.Ala220Ser | 1.0 |
Pf3D7_07_v3 | 405362 | PF3D7_0709000 | CRT | p.Asn326Ser | 1.0 |
Pf3D7_08_v3 | 548068 | PF3D7_0810800 | PPPK-DHPS | c.-131_-130delAT | 1.0 |
Pf3D7_08_v3 | 643630 | PF3D7_0813000 | PF3D7_0813000 | p.Asn419Ser | 0.19 |
Pf3D7_08_v3 | 643671 | PF3D7_0813000 | PF3D7_0813000 | c.1215C>T | 0.29 |
Pf3D7_08_v3 | 643675 | PF3D7_0813000 | PF3D7_0813000 | p.Ser404Asn | 0.21 |
Pf3D7_08_v3 | 643680 | PF3D7_0813000 | PF3D7_0813000 | c.1206T>C | 0.19 |
Pf3D7_08_v3 | 644336 | PF3D7_0813000 | PF3D7_0813000 | c.538_549delAGAGATAGAACA | 1.0 |
Pf3D7_10_v3 | 1047084 | PF3D7_1025000 | PF3D7_1025000 | p.Asn566Asp | 0.38 |
Pf3D7_10_v3 | 1047087 | PF3D7_1025000 | PF3D7_1025000 | p.Asn565Asp | 0.29 |
Pf3D7_10_v3 | 1047095 | PF3D7_1025000 | PF3D7_1025000 | c.1682_1684dupATA | 1.0 |
Pf3D7_10_v3 | 1047391 | PF3D7_1025000 | PF3D7_1025000 | c.1383_1388delAGATAA | 0.35 |
Pf3D7_10_v3 | 1047391 | PF3D7_1025000 | PF3D7_1025000 | c.1383_1388delAGATAA | 0.35 |
Pf3D7_10_v3 | 1049827 | PF3D7_1025000 | PF3D7_1025000 | c.-67G>A | 0.17 |
Pf3D7_10_v3 | 1450480 | PF3D7_1036800 | PF3D7_1036800 | p.Ser181Phe | 0.5 |
Pf3D7_10_v3 | 1451781 | PF3D7_1036800 | PF3D7_1036800 | c.-136delT | 0.4 |
Pf3D7_11_v3 | 1526429 | PF3D7_1138700 | PF3D7_1138700 | p.Ser1613Asn | 0.17 |
Pf3D7_11_v3 | 1529377 | PF3D7_1138700 | PF3D7_1138700 | c.1890C>T | 0.16 |
Pf3D7_12_v3 | 717853 | PF3D7_1218300 | AP2-MU | c.-102_-101insT | 1.0 |
Pf3D7_12_v3 | 717865 | PF3D7_1218300 | AP2-MU | c.-90_-89insTATATT | 1.0 |
Pf3D7_12_v3 | 1925560 | PF3D7_1246300 | PF3D7_1246300 | c.-81_-80delTA | 1.0 |
Pf3D7_12_v3 | 2091905 | PF3D7_1251200 | PF3D7_1251200 | c.-182_-181insTATA | 1.0 |
Pf3D7_12_v3 | 2094061 | PF3D7_1251200 | PF3D7_1251200 | c.1657_1659delAAT | 0.16 |
Pf3D7_13_v3 | 748998 | PF3D7_1318100 | PF3D7_1318100 | c.-28delA | 0.25 |
Pf3D7_13_v3 | 848114 | PF3D7_1320600 | RAB11a | p.Gln181Lys | 0.3 |
Pf3D7_13_v3 | 1727052 | PF3D7_1343700 | K13 | c.-55A>T | 1.0 |
Pf3D7_13_v3 | 1727056 | PF3D7_1343700 | K13 | c.-59A>T | 1.0 |
Pf3D7_13_v3 | 1727073 | PF3D7_1343700 | K13 | c.-76T>A | 1.0 |
Pf3D7_13_v3 | 1727101 | PF3D7_1343700 | K13 | c.-104A>T | 1.0 |
Pf3D7_14_v3 | 1548826 | PF3D7_1438400 | MCA2 | c.-91_-89delAAA | 0.4 |
Pf3D7_14_v3 | 1548826 | PF3D7_1438400 | MCA2 | c.-92G>A | 0.6 |
Pf3D7_14_v3 | 1548826 | PF3D7_1438400 | MCA2 | c.-91_-89delAAA | 0.4 |
Pf3D7_14_v3 | 1548826 | PF3D7_1438400 | MCA2 | c.-92G>A | 0.6 |
Pf3D7_14_v3 | 1550927 | PF3D7_1438400 | MCA2 | p.Ser305Asn | 0.21 |
Pf3D7_14_v3 | 1550945 | PF3D7_1438400 | MCA2 | p.Ser311Asn | 0.31 |
Pf3D7_14_v3 | 1552502 | PF3D7_1438400 | MCA2 | c.2501delA | 0.19 |
Pf3D7_14_v3 | 1556519 | PF3D7_1438400 | MCA2 | c.6000T>C | 1.0 |
Pf3D7_14_v3 | 2481070 | PF3D7_1460900 | ARPS10 | p.Val127Met | 1.0 |
Pf3D7_14_v3 | 2481073 | PF3D7_1460900 | ARPS10 | p.Asp128His | 1.0 |
Chromosome | Position | Depth | Annotation |
---|---|---|---|
Pf3D7_07_v3 | 404407 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 404408 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 404409 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 405361 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 405362 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_07_v3 | 405363 | 7 | Type: drug_resistance, Drug: chloroquine, Source: https://www.who.int/publications/i/item/9789240012813 |
Pf3D7_13_v3 | 1724975 | 7 | Type: drug_resistance, Drug: artemisinin, Source: https://www.who.int/publications/i/item/9789240012813 |
Resistance variants report
Gene | Mutations |
---|---|
DHFR-TS |
p.Asn51Ile
p.Cys59Arg
p.Ser108Asn
p.Ile164Leu
|
MDR1 |
p.Tyr184Phe
|
CRT |
p.Lys76Thr
p.Gln271Glu
p.Ile356Thr
p.Arg371Ile
|
PPPK-DHPS |
p.Ser436Ala
p.Ala437Gly
|
Other variants
Gene | ([{'chrom': 'Pf3D7_01_v3', 'pos': 190143, 'ref': 'C', 'alt': 'CAT', 'depth': 17, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'upstream_gene_variant', 'change': 'c.-126_-125insAT', 'nucleotide_change': 'c.-126_-125insAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-126_-125insAT', 'protein_change': '', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 190260, 'ref': 'G', 'alt': 'A', 'depth': 25, 'freq': 0.96, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'upstream_gene_variant', 'change': 'c.-9G>A', 'nucleotide_change': 'c.-9G>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-9G>A', 'protein_change': '', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 190616, 'ref': 'A', 'alt': 'G', 'depth': 25, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 19, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'change': 'c.348A>G', 'nucleotide_change': 'c.348A>G', 'protein_change': 'p.Thr116Thr', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'nucleotide_change': 'c.348A>G', 'protein_change': 'p.Thr116Thr', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 191282, 'ref': 'C', 'alt': 'T', 'depth': 29, 'freq': 0.41, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'change': 'c.1014C>T', 'nucleotide_change': 'c.1014C>T', 'protein_change': 'p.Asp338Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1014C>T', 'protein_change': 'p.Asp338Asp', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 191685, 'ref': 'TATA', 'alt': 'T', 'depth': 20, 'freq': 0.95, 'sv': False, 'filter': 'pass', 'forward_reads': 9, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'conservative_inframe_deletion', 'change': 'c.1444_1446delAAT', 'nucleotide_change': 'c.1444_1446delAAT', 'protein_change': 'p.Asn482del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'conservative_inframe_deletion', 'nucleotide_change': 'c.1444_1446delAAT', 'protein_change': 'p.Asn482del', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 192111, 'ref': 'T', 'alt': 'C', 'depth': 44, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 21, 'reverse_reads': 23, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Tyr615His', 'nucleotide_change': 'c.1843T>C', 'protein_change': 'p.Tyr615His', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.1843T>C', 'protein_change': 'p.Tyr615His', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 192633, 'ref': 'A', 'alt': 'G', 'depth': 23, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 13, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Asn789Asp', 'nucleotide_change': 'c.2365A>G', 'protein_change': 'p.Asn789Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.2365A>G', 'protein_change': 'p.Asn789Asp', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 193167, 'ref': 'A', 'alt': 'G', 'depth': 23, 'freq': 0.96, 'sv': False, 'filter': 'pass', 'forward_reads': 7, 'reverse_reads': 15, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Met967Val', 'nucleotide_change': 'c.2899A>G', 'protein_change': 'p.Met967Val', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.2899A>G', 'protein_change': 'p.Met967Val', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 193299, 'ref': 'G', 'alt': 'A', 'depth': 30, 'freq': 0.97, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Glu1011Lys', 'nucleotide_change': 'c.3031G>A', 'protein_change': 'p.Glu1011Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.3031G>A', 'protein_change': 'p.Glu1011Lys', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 193667, 'ref': 'G', 'alt': 'C', 'depth': 28, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Arg1133Ser', 'nucleotide_change': 'c.3399G>C', 'protein_change': 'p.Arg1133Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.3399G>C', 'protein_change': 'p.Arg1133Ser', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 194117, 'ref': 'T', 'alt': 'C', 'depth': 21, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 17, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'change': 'c.3849T>C', 'nucleotide_change': 'c.3849T>C', 'protein_change': 'p.Phe1283Phe', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'synonymous_variant', 'nucleotide_change': 'c.3849T>C', 'protein_change': 'p.Phe1283Phe', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 194843, 'ref': 'CAAATATGAA', 'alt': 'C', 'depth': 15, 'freq': 0.67, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'change': 'c.4593_4601delAAAATATGA', 'nucleotide_change': 'c.4593_4601delAAAATATGA', 'protein_change': 'p.Glu1531_Tyr1533del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.4593_4601delAAAATATGA', 'protein_change': 'p.Glu1531_Tyr1533del', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 194843, 'ref': 'CAAATATGAA', 'alt': 'C', 'depth': 15, 'freq': 0.67, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'change': 'c.4593_4601delAAAATATGA', 'nucleotide_change': 'c.4593_4601delAAAATATGA', 'protein_change': 'p.Glu1531_Tyr1533del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.4593_4601delAAAATATGA', 'protein_change': 'p.Glu1531_Tyr1533del', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 196010, 'ref': 'A', 'alt': 'C', 'depth': 27, 'freq': 0.78, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Lys1914Asn', 'nucleotide_change': 'c.5742A>C', 'protein_change': 'p.Lys1914Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.5742A>C', 'protein_change': 'p.Lys1914Asn', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 196011, 'ref': 'G', 'alt': 'A', 'depth': 26, 'freq': 0.77, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Glu1915Lys', 'nucleotide_change': 'c.5743G>A', 'protein_change': 'p.Glu1915Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.5743G>A', 'protein_change': 'p.Glu1915Lys', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 196981, 'ref': 'G', 'alt': 'A', 'depth': 18, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 12, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Arg2238Lys', 'nucleotide_change': 'c.6713G>A', 'protein_change': 'p.Arg2238Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.6713G>A', 'protein_change': 'p.Arg2238Lys', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 201154, 'ref': 'T', 'alt': 'C', 'depth': 25, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 19, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Leu3475Ser', 'nucleotide_change': 'c.10424T>C', 'protein_change': 'p.Leu3475Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.10424T>C', 'protein_change': 'p.Leu3475Ser', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_03_v3', 'pos': 922867, 'ref': 'CAT', 'alt': 'C', 'depth': 20, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 14, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'upstream_gene_variant', 'change': 'c.-106_-105delAT', 'nucleotide_change': 'c.-106_-105delAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-106_-105delAT', 'protein_change': '', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_03_v3', 'pos': 924907, 'ref': 'G', 'alt': 'T', 'depth': 31, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 14, 'reverse_reads': 17, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'synonymous_variant', 'change': 'c.1806G>T', 'nucleotide_change': 'c.1806G>T', 'protein_change': 'p.Ser602Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1806G>T', 'protein_change': 'p.Ser602Ser', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_03_v3', 'pos': 925808, 'ref': 'A', 'alt': 'G', 'depth': 44, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 24, 'reverse_reads': 20, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'missense_variant', 'change': 'p.Lys903Glu', 'nucleotide_change': 'c.2707A>G', 'protein_change': 'p.Lys903Glu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'missense_variant', 'nucleotide_change': 'c.2707A>G', 'protein_change': 'p.Lys903Glu', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_03_v3', 'pos': 925890, 'ref': 'TTAATAA', 'alt': 'T', 'depth': 32, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 19, 'reverse_reads': 13, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'disruptive_inframe_deletion', 'change': 'c.2804_2809delATAATA', 'nucleotide_change': 'c.2804_2809delATAATA', 'protein_change': 'p.Asn935_Asn936del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.2804_2809delATAATA', 'protein_change': 'p.Asn935_Asn936del', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_03_v3', 'pos': 925967, 'ref': 'G', 'alt': 'A', 'depth': 30, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 22, 'sv_len': None, 'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'missense_variant', 'change': 'p.Glu956Lys', 'nucleotide_change': 'c.2866G>A', 'protein_change': 'p.Glu956Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0321900', 'feature_id': 'transcript:PF3D7_0321900', 'type': 'missense_variant', 'nucleotide_change': 'c.2866G>A', 'protein_change': 'p.Glu956Lys', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_05_v3', 'pos': 410184, 'ref': 'C', 'alt': 'A', 'depth': 13, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 9, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'upstream_gene_variant', 'change': 'c.-84C>A', 'nucleotide_change': 'c.-84C>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-84C>A', 'protein_change': '', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 410338, 'ref': 'A', 'alt': 'T', 'depth': 28, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'change': 'p.His24Leu', 'nucleotide_change': 'c.71A>T', 'protein_change': 'p.His24Leu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'nucleotide_change': 'c.71A>T', 'protein_change': 'p.His24Leu', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 410566, 'ref': 'T', 'alt': 'C', 'depth': 25, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 19, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'change': 'p.Val100Ala', 'nucleotide_change': 'c.299T>C', 'protein_change': 'p.Val100Ala', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'nucleotide_change': 'c.299T>C', 'protein_change': 'p.Val100Ala', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 412910, 'ref': 'CAACAAC', 'alt': 'CAATAAT', 'depth': 14, 'freq': 0.5, 'sv': False, 'filter': 'pass', 'forward_reads': 3, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'change': 'c.2646_2649delCAACinsTAAT', 'nucleotide_change': 'c.2646_2649delCAACinsTAAT', 'protein_change': 'p.884', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.2646_2649delCAACinsTAAT', 'protein_change': 'p.884', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 413414, 'ref': 'T', 'alt': 'C', 'depth': 16, 'freq': 0.56, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'change': 'c.3147T>C', 'nucleotide_change': 'c.3147T>C', 'protein_change': 'p.Asp1049Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.3147T>C', 'protein_change': 'p.Asp1049Asp', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 959840, 'ref': 'G', 'alt': 'A', 'depth': 30, 'freq': 0.43, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 5, 'sv_len': None, 'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'missense_variant', 'change': 'p.Asp651Asn', 'nucleotide_change': 'c.1951G>A', 'protein_change': 'p.Asp651Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'missense_variant', 'nucleotide_change': 'c.1951G>A', 'protein_change': 'p.Asp651Asn', 'annotation': [], 'gene': 'MDR1'}], 'gene': 'MDR1'}, {'chrom': 'Pf3D7_07_v3', 'pos': 403620, 'ref': 'GA', 'alt': 'TG', 'depth': 12, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0709000', 'feature_id': 'transcript:PF3D7_0709000', 'type': 'missense_variant', 'change': 'p.MetAsn74IleAsp', 'nucleotide_change': 'c.222_223delGAinsTG', 'protein_change': 'p.MetAsn74IleAsp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0709000', 'feature_id': 'transcript:PF3D7_0709000', 'type': 'missense_variant', 'nucleotide_change': 'c.222_223delGAinsTG', 'protein_change': 'p.MetAsn74IleAsp', 'annotation': [], 'gene': 'CRT'}], 'gene': 'CRT'}, {'chrom': 'Pf3D7_07_v3', 'pos': 403623, 'ref': 'T', 'alt': 'A', 'depth': 11, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 3, 'sv_len': None, 'gene_id': 'PF3D7_0709000', 'feature_id': 'transcript:PF3D7_0709000', 'type': 'missense_variant', 'change': 'p.Asn75Lys', 'nucleotide_change': 'c.225T>A', 'protein_change': 'p.Asn75Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0709000', 'feature_id': 'transcript:PF3D7_0709000', 'type': 'missense_variant', 'nucleotide_change': 'c.225T>A', 'protein_change': 'p.Asn75Lys', 'annotation': [], 'gene': 'CRT'}], 'gene': 'CRT'}, {'chrom': 'Pf3D7_08_v3', 'pos': 643648, 'ref': 'C', 'alt': 'T', 'depth': 39, 'freq': 0.49, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'missense_variant', 'change': 'p.Ser413Asn', 'nucleotide_change': 'c.1238G>A', 'protein_change': 'p.Ser413Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'missense_variant', 'nucleotide_change': 'c.1238G>A', 'protein_change': 'p.Ser413Asn', 'annotation': [], 'gene': 'PF3D7_0813000'}], 'gene': 'PF3D7_0813000'}, {'chrom': 'Pf3D7_08_v3', 'pos': 644936, 'ref': 'G', 'alt': 'T', 'depth': 15, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'upstream_gene_variant', 'change': 'c.-51C>A', 'nucleotide_change': 'c.-51C>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-51C>A', 'protein_change': '', 'annotation': [], 'gene': 'PF3D7_0813000'}], 'gene': 'PF3D7_0813000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1045876, 'ref': 'G', 'alt': 'C', 'depth': 12, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Gln932Glu', 'nucleotide_change': 'c.2794C>G', 'protein_change': 'p.Gln932Glu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.2794C>G', 'protein_change': 'p.Gln932Glu', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1046056, 'ref': 'G', 'alt': 'C', 'depth': 24, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 15, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'change': 'c.2724C>G', 'nucleotide_change': 'c.2724C>G', 'protein_change': 'p.Thr908Thr', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'nucleotide_change': 'c.2724C>G', 'protein_change': 'p.Thr908Thr', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047323, 'ref': 'A', 'alt': 'G', 'depth': 32, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 21, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Phe486Ser', 'nucleotide_change': 'c.1457T>C', 'protein_change': 'p.Phe486Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1457T>C', 'protein_change': 'p.Phe486Ser', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047391, 'ref': 'TTTATCT', 'alt': 'TTTATCC', 'depth': 20, 'freq': 0.65, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 3, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'change': 'c.1383A>G', 'nucleotide_change': 'c.1383A>G', 'protein_change': 'p.Lys461Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1383A>G', 'protein_change': 'p.Lys461Lys', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047391, 'ref': 'TTTATCT', 'alt': 'TTTATCC', 'depth': 20, 'freq': 0.65, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 3, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'change': 'c.1383A>G', 'nucleotide_change': 'c.1383A>G', 'protein_change': 'p.Lys461Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1383A>G', 'protein_change': 'p.Lys461Lys', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1049903, 'ref': 'AAT', 'alt': 'A', 'depth': 18, 'freq': 0.94, 'sv': False, 'filter': 'pass', 'forward_reads': 9, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'upstream_gene_variant', 'change': 'c.-145_-144delAT', 'nucleotide_change': 'c.-145_-144delAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-145_-144delAT', 'protein_change': '', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1449646, 'ref': 'G', 'alt': 'A', 'depth': 36, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 16, 'reverse_reads': 20, 'sv_len': None, 'gene_id': 'PF3D7_1036800', 'feature_id': 'transcript:PF3D7_1036800', 'type': 'missense_variant', 'change': 'p.Thr459Ile', 'nucleotide_change': 'c.1376C>T', 'protein_change': 'p.Thr459Ile', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1036800', 'feature_id': 'transcript:PF3D7_1036800', 'type': 'missense_variant', 'nucleotide_change': 'c.1376C>T', 'protein_change': 'p.Thr459Ile', 'annotation': [], 'gene': 'PF3D7_1036800'}], 'gene': 'PF3D7_1036800'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1526106, 'ref': 'A', 'alt': 'C', 'depth': 42, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 22, 'reverse_reads': 20, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'change': 'p.Ser1721Ala', 'nucleotide_change': 'c.5161T>G', 'protein_change': 'p.Ser1721Ala', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'nucleotide_change': 'c.5161T>G', 'protein_change': 'p.Ser1721Ala', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1529369, 'ref': 'C', 'alt': 'T', 'depth': 25, 'freq': 0.8, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 7, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'change': 'p.Ser633Asn', 'nucleotide_change': 'c.1898G>A', 'protein_change': 'p.Ser633Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'nucleotide_change': 'c.1898G>A', 'protein_change': 'p.Ser633Asn', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1529778, 'ref': 'C', 'alt': 'G', 'depth': 40, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 22, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'change': 'p.Glu497Gln', 'nucleotide_change': 'c.1489G>C', 'protein_change': 'p.Glu497Gln', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'nucleotide_change': 'c.1489G>C', 'protein_change': 'p.Glu497Gln', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1530261, 'ref': 'C', 'alt': 'G', 'depth': 36, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'change': 'p.Glu336Gln', 'nucleotide_change': 'c.1006G>C', 'protein_change': 'p.Glu336Gln', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'nucleotide_change': 'c.1006G>C', 'protein_change': 'p.Glu336Gln', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_12_v3', 'pos': 211053, 'ref': 'CAT', 'alt': 'C', 'depth': 19, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 14, 'sv_len': None, 'gene_id': 'PF3D7_1204400', 'feature_id': 'transcript:PF3D7_1204400', 'type': 'upstream_gene_variant', 'change': 'c.-162_-161delAT', 'nucleotide_change': 'c.-162_-161delAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1204400', 'feature_id': 'transcript:PF3D7_1204400', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-162_-161delAT', 'protein_change': '', 'annotation': [], 'gene': 'PF3D7_1204400'}], 'gene': 'PF3D7_1204400'}, {'chrom': 'Pf3D7_12_v3', 'pos': 529418, 'ref': 'C', 'alt': 'T', 'depth': 16, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'missense_variant', 'change': 'p.Gly1128Arg', 'nucleotide_change': 'c.3382G>A', 'protein_change': 'p.Gly1128Arg', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'missense_variant', 'nucleotide_change': 'c.3382G>A', 'protein_change': 'p.Gly1128Arg', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 532131, 'ref': 'G', 'alt': 'T', 'depth': 23, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'synonymous_variant', 'change': 'c.669C>A', 'nucleotide_change': 'c.669C>A', 'protein_change': 'p.Gly223Gly', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'synonymous_variant', 'nucleotide_change': 'c.669C>A', 'protein_change': 'p.Gly223Gly', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 532889, 'ref': 'GATATAGAT', 'alt': 'G', 'depth': 13, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 9, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'upstream_gene_variant', 'change': 'c.-98_-91delATCTATAT', 'nucleotide_change': 'c.-98_-91delATCTATAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-98_-91delATCTATAT', 'protein_change': '', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 591301, 'ref': 'T', 'alt': 'C', 'depth': 24, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'synonymous_variant', 'change': 'c.1134A>G', 'nucleotide_change': 'c.1134A>G', 'protein_change': 'p.Leu378Leu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1134A>G', 'protein_change': 'p.Leu378Leu', 'annotation': [], 'gene': 'PRS'}], 'gene': 'PRS'}, {'chrom': 'Pf3D7_12_v3', 'pos': 592329, 'ref': 'C', 'alt': 'T', 'depth': 39, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 21, 'sv_len': None, 'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'missense_variant', 'change': 'p.Val36Ile', 'nucleotide_change': 'c.106G>A', 'protein_change': 'p.Val36Ile', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'missense_variant', 'nucleotide_change': 'c.106G>A', 'protein_change': 'p.Val36Ile', 'annotation': [], 'gene': 'PRS'}], 'gene': 'PRS'}, {'chrom': 'Pf3D7_12_v3', 'pos': 592496, 'ref': 'C', 'alt': 'T', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'upstream_gene_variant', 'change': 'c.-62G>A', 'nucleotide_change': 'c.-62G>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-62G>A', 'protein_change': '', 'annotation': [], 'gene': 'PRS'}], 'gene': 'PRS'}, {'chrom': 'Pf3D7_12_v3', 'pos': 718631, 'ref': 'TTAA', 'alt': 'T', 'depth': 19, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_1218300', 'feature_id': 'transcript:PF3D7_1218300', 'type': 'disruptive_inframe_deletion', 'change': 'c.699_701delTAA', 'nucleotide_change': 'c.699_701delTAA', 'protein_change': 'p.Asn233del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1218300', 'feature_id': 'transcript:PF3D7_1218300', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.699_701delTAA', 'protein_change': 'p.Asn233del', 'annotation': [], 'gene': 'AP2-MU'}], 'gene': 'AP2-MU'}, {'chrom': 'Pf3D7_12_v3', 'pos': 1927229, 'ref': 'T', 'alt': 'C', 'depth': 28, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_1246300', 'feature_id': 'transcript:PF3D7_1246300', 'type': 'synonymous_variant', 'change': 'c.1041T>C', 'nucleotide_change': 'c.1041T>C', 'protein_change': 'p.Phe347Phe', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1246300', 'feature_id': 'transcript:PF3D7_1246300', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1041T>C', 'protein_change': 'p.Phe347Phe', 'annotation': [], 'gene': 'PF3D7_1246300'}], 'gene': 'PF3D7_1246300'}, {'chrom': 'Pf3D7_12_v3', 'pos': 2093058, 'ref': 'A', 'alt': 'G', 'depth': 27, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 16, 'sv_len': None, 'gene_id': 'PF3D7_1251200', 'feature_id': 'transcript:PF3D7_1251200', 'type': 'synonymous_variant', 'change': 'c.636A>G', 'nucleotide_change': 'c.636A>G', 'protein_change': 'p.Lys212Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1251200', 'feature_id': 'transcript:PF3D7_1251200', 'type': 'synonymous_variant', 'nucleotide_change': 'c.636A>G', 'protein_change': 'p.Lys212Lys', 'annotation': [], 'gene': 'PF3D7_1251200'}], 'gene': 'PF3D7_1251200'}, {'chrom': 'Pf3D7_13_v3', 'pos': 1726571, 'ref': 'G', 'alt': 'GATTATT', 'depth': 16, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 7, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'conservative_inframe_insertion', 'change': 'c.421_426dupAATAAT', 'nucleotide_change': 'c.421_426dupAATAAT', 'protein_change': 'p.Asn141_Asn142dup', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'conservative_inframe_insertion', 'nucleotide_change': 'c.421_426dupAATAAT', 'protein_change': 'p.Asn141_Asn142dup', 'annotation': [], 'gene': 'K13'}], 'gene': 'K13'}, {'chrom': 'Pf3D7_13_v3', 'pos': 1727145, 'ref': 'G', 'alt': 'T', 'depth': 17, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'change': 'c.-148C>A', 'nucleotide_change': 'c.-148C>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-148C>A', 'protein_change': '', 'annotation': [], 'gene': 'K13'}], 'gene': 'K13'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550187, 'ref': 'T', 'alt': 'G', 'depth': 36, 'freq': 0.97, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 15, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'change': 'c.174T>G', 'nucleotide_change': 'c.174T>G', 'protein_change': 'p.Ser58Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'nucleotide_change': 'c.174T>G', 'protein_change': 'p.Ser58Ser', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550518, 'ref': 'GTGAATAATA', 'alt': 'ATGAATAATG', 'depth': 19, 'freq': 0.42, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.ValAsnAsnMet169MetAsnAsnVal', 'nucleotide_change': 'c.505_514delGTGAATAATAinsATGAATAATG', 'protein_change': 'p.ValAsnAsnMet169MetAsnAsnVal', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.505_514delGTGAATAATAinsATGAATAATG', 'protein_change': 'p.ValAsnAsnMet169MetAsnAsnVal', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550518, 'ref': 'GTGAATAATA', 'alt': 'G', 'depth': 19, 'freq': 0.58, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 7, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'conservative_inframe_deletion', 'change': 'c.514_522delATGAATAAT', 'nucleotide_change': 'c.514_522delATGAATAAT', 'protein_change': 'p.Met172_Asn174del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'conservative_inframe_deletion', 'nucleotide_change': 'c.514_522delATGAATAAT', 'protein_change': 'p.Met172_Asn174del', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550893, 'ref': 'TATA', 'alt': 'T', 'depth': 14, 'freq': 0.93, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 8, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'conservative_inframe_deletion', 'change': 'c.904_906delAAT', 'nucleotide_change': 'c.904_906delAAT', 'protein_change': 'p.Asn302del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'conservative_inframe_deletion', 'nucleotide_change': 'c.904_906delAAT', 'protein_change': 'p.Asn302del', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550934, 'ref': 'T', 'alt': 'C', 'depth': 16, 'freq': 0.69, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 7, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'change': 'c.921T>C', 'nucleotide_change': 'c.921T>C', 'protein_change': 'p.Asn307Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'nucleotide_change': 'c.921T>C', 'protein_change': 'p.Asn307Asn', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550938, 'ref': 'G', 'alt': 'A', 'depth': 15, 'freq': 0.6, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 5, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.Val309Ile', 'nucleotide_change': 'c.925G>A', 'protein_change': 'p.Val309Ile', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.925G>A', 'protein_change': 'p.Val309Ile', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550959, 'ref': 'TATA', 'alt': 'T', 'depth': 14, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 3, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'disruptive_inframe_deletion', 'change': 'c.960_962delTAA', 'nucleotide_change': 'c.960_962delTAA', 'protein_change': 'p.Asn321del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.960_962delTAA', 'protein_change': 'p.Asn321del', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1553266, 'ref': 'A', 'alt': 'G', 'depth': 38, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 15, 'reverse_reads': 23, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.Asn1085Asp', 'nucleotide_change': 'c.3253A>G', 'protein_change': 'p.Asn1085Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.3253A>G', 'protein_change': 'p.Asn1085Asp', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1553697, 'ref': 'C', 'alt': 'T', 'depth': 24, 'freq': 0.96, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'change': 'c.3684C>T', 'nucleotide_change': 'c.3684C>T', 'protein_change': 'p.His1228His', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'nucleotide_change': 'c.3684C>T', 'protein_change': 'p.His1228His', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}], {'chrom': 'Chromosome:', 'pos': 'Genome Position', 'gene_id': 'Locus Tag', 'gene': 'Gene Name', 'change': 'Change', 'freq': 'Estimated fraction'}, 'Other variants', Undefined)Mutations |
---|---|
UBP1 |
c.-126_-125insAT
c.-9G>A
c.348A>G
c.1014C>T
c.1444_1446delAAT
p.Tyr615His
p.Asn789Asp
p.Met967Val
p.Glu1011Lys
p.Arg1133Ser
c.3849T>C
c.4593_4601delAAAATATGA
c.4593_4601delAAAATATGA
p.Lys1914Asn
p.Glu1915Lys
p.Arg2238Lys
p.Leu3475Ser
|
CARL |
c.-106_-105delAT
c.1806G>T
p.Lys903Glu
c.2804_2809delATAATA
p.Glu956Lys
|
PI4K |
c.-84C>A
p.His24Leu
p.Val100Ala
c.2646_2649delCAACinsTAAT
c.3147T>C
|
MDR1 |
p.Asp651Asn
|
CRT |
p.MetAsn74IleAsp
p.Asn75Lys
|
PF3D7_0813000 |
p.Ser413Asn
c.-51C>A
|
PF3D7_1025000 |
p.Gln932Glu
c.2724C>G
p.Phe486Ser
c.1383A>G
c.1383A>G
c.-145_-144delAT
|
PF3D7_1036800 |
p.Thr459Ile
|
PF3D7_1138700 |
p.Ser1721Ala
p.Ser633Asn
p.Glu497Gln
p.Glu336Gln
|
PF3D7_1204400 |
c.-162_-161delAT
|
ATP4 |
p.Gly1128Arg
c.669C>A
c.-98_-91delATCTATAT
|
PRS |
c.1134A>G
p.Val36Ile
c.-62G>A
|
AP2-MU |
c.699_701delTAA
|
PF3D7_1246300 |
c.1041T>C
|
PF3D7_1251200 |
c.636A>G
|
K13 |
c.421_426dupAATAAT
c.-148C>A
|
MCA2 |
c.174T>G
p.ValAsnAsnMet169MetAsnAsnVal
c.514_522delATGAATAAT
c.904_906delAAT
c.921T>C
p.Val309Ile
c.960_962delTAA
p.Asn1085Asp
c.3684C>T
|
QC failed variants
Gene | Mutations |
---|---|
UBP1 |
|
DHFR-TS |
|
PI4K |
|
MDR1 |
|
CRT |
|
PPPK-DHPS |
|
PF3D7_0813000 |
|
PF3D7_1025000 |
|
PF3D7_1036800 |
|
PF3D7_1138700 |
|
AP2-MU |
|
PF3D7_1246300 |
|
PF3D7_1251200 |
|
PF3D7_1318100 |
|
RAB11a |
|
K13 |
|
MCA2 |
|
ARPS10 |
|
Missing positions report
Gene | Mutations |
---|---|
|
Southeast Asia - 90.0%
Process | Software |
---|---|
|
|
|
|
|
|
|
|
Gene | Percentage depth passed | Median Depth |
---|---|---|
UBP1 | 96.43 | 29.0 |
PF3D7_0109800 | 95.25 | 29.0 |
CARL | 87.69 | 25.0 |
DHFR-TS | 95.76 | 28.0 |
PI4K | 89.4 | 26.0 |
MDR1 | 99.64 | 34.0 |
DHODH | 89.72 | 33.0 |
CRT | 73.57 | 15.0 |
PPPK-DHPS | 95.95 | 28.0 |
PF3D7_0813000 | 89.55 | 25.0 |
PF3D7_1025000 | 84.52 | 26.0 |
PF3D7_1036800 | 88.7 | 22.0 |
PF3D7_1113300 | 91.13 | 28.0 |
PF3D7_1138700 | 94.08 | 33.0 |
PF3D7_1204400 | 81.82 | 19.0 |
ATP4 | 99.64 | 29.0 |
PRS | 97.05 | 31.0 |
AP2-MU | 92.41 | 29.0 |
PF3D7_1246300 | 83.49 | 18.0 |
PF3D7_1251200 | 87.03 | 26.0 |
PF3D7_1318100 | 97.26 | 24.0 |
RAB11a | 84.42 | 17.0 |
K13 | 97.23 | 30.0 |
MCA2 | 96.75 | 30.0 |
eEF2 | 95.9 | 23.0 |
ARPS10 | 73.95 | 13.0 |
CYTB | 100.0 | 385.0 |
Plasmodium falciparum
Species | Prediction |
---|---|
Plasmodium falciparum |
99.76 |