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FASTQ FILE NAME: Example file

Species view

What species is your sample at 99% accuracy

Species

Plasmodium falciparum

Species	Prediction
Plasmodium falciparum	99.76 %

Genomic variants

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

Genomic variants

Resistance report

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

Other variants

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

Missing positions report

Chromosome	Position	Depth	Gene	Annotation	Drug related	Variant
Pf3D7_07_v3	404407	7	PF3D7_0709000	drug resistance	chloroquine	p.Ala220Ser
Pf3D7_07_v3	404408	7	PF3D7_0709000	drug resistance	chloroquine	p.Ala220Ser
Pf3D7_07_v3	404409	7	PF3D7_0709000	drug resistance	chloroquine	p.Ala220Ser
Pf3D7_07_v3	405361	7	PF3D7_0709000	drug resistance	chloroquine	p.Asn326Ser
Pf3D7_07_v3	405362	7	PF3D7_0709000	drug resistance	chloroquine	p.Asn326Ser
Pf3D7_07_v3	405363	7	PF3D7_0709000	drug resistance	chloroquine	p.Asn326Ser
Pf3D7_13_v3	1724975	7	PF3D7_1343700	drug resistance	artemisinin	p.Ala675Val

QC failed variants

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 REPORT OTHER VARIANTS MISSING POSITIONS

QC FAIL VARIANTS

Resistance variants report

Gene	Mutations
DHFR-TS	p.Asn51Ile p.Cys59Arg p.Ser108Asn p.Ile164Leu VIEW IN IGV
MDR1	p.Tyr184Phe VIEW IN IGV
CRT	p.Lys76Thr p.Gln271Glu p.Ile356Thr p.Arg371Ile VIEW IN IGV
PPPK-DHPS	p.Ser436Ala p.Ala437Gly VIEW IN IGV

Other variants

([{'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')

Gene	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 VIEW IN IGV
CARL	c.-106_-105delAT c.1806G>T p.Lys903Glu c.2804_2809delATAATA p.Glu956Lys VIEW IN IGV
PI4K	c.-84C>A p.His24Leu p.Val100Ala c.2646_2649delCAACinsTAAT c.3147T>C VIEW IN IGV
MDR1	p.Asp651Asn VIEW IN IGV
CRT	p.MetAsn74IleAsp p.Asn75Lys VIEW IN IGV
PF3D7_0813000	p.Ser413Asn c.-51C>A VIEW IN IGV
PF3D7_1025000	p.Gln932Glu c.2724C>G p.Phe486Ser c.1383A>G c.1383A>G c.-145_-144delAT VIEW IN IGV
PF3D7_1036800	p.Thr459Ile VIEW IN IGV
PF3D7_1138700	p.Ser1721Ala p.Ser633Asn p.Glu497Gln p.Glu336Gln VIEW IN IGV
PF3D7_1204400	c.-162_-161delAT VIEW IN IGV
ATP4	p.Gly1128Arg c.669C>A c.-98_-91delATCTATAT VIEW IN IGV
PRS	c.1134A>G p.Val36Ile c.-62G>A VIEW IN IGV
AP2-MU	c.699_701delTAA VIEW IN IGV
PF3D7_1246300	c.1041T>C VIEW IN IGV
PF3D7_1251200	c.636A>G VIEW IN IGV
K13	c.421_426dupAATAAT c.-148C>A VIEW IN IGV
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 VIEW IN IGV

QC failed variants

Gene	Mutations
UBP1	VIEW IN IGV
DHFR-TS	VIEW IN IGV
PI4K	VIEW IN IGV
MDR1	VIEW IN IGV
CRT	VIEW IN IGV
PPPK-DHPS	VIEW IN IGV
PF3D7_0813000	VIEW IN IGV
PF3D7_1025000	VIEW IN IGV
PF3D7_1036800	VIEW IN IGV
PF3D7_1138700	VIEW IN IGV
AP2-MU	VIEW IN IGV
PF3D7_1246300	VIEW IN IGV
PF3D7_1251200	VIEW IN IGV
PF3D7_1318100	VIEW IN IGV
RAB11a	VIEW IN IGV
K13	VIEW IN IGV
MCA2	VIEW IN IGV
ARPS10	VIEW IN IGV

Missing positions report

Gene	Mutations
	VIEW IN IGV

Sample location

Where your sample is from

Estimated Region of Origin

Southeast Asia - 90.0%

Percentage of barcoding SNPs that have coverage: 100 %

Tools used

What was used to analyse your sample

moi	Haplotype counts	Software	Software version
4	1: 6 2: 24 3: 7 4: 6 5: 2	pymoi	0.1.1

Coverage Report

This section shows the average number of reads that align to, or 'cover', known reference bases

Gene	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

SEE ALL

Coverage report

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

IGV

View certain areas of interest using IGV

RESULT ID

SPECIES

GENOMIC VARIANTS

ESTIMATED ORIGIN OF REGION

EST MOI

COVERAGE REPORT

SHOW MORE INFO

RESULT ID: cefa3f2e-d334-4fa5-91ac-920f39cc11a0

Identifier	Date
Cefa3f2e-D334-4fa5-91ac-920f39cc11a0	Wed Mar 12 04:22:34 2025

BACK

Species

Plasmodium falciparum

Species	Prediction
Plasmodium falciparum	99.76 %

BACK

Genomic variants

Resistance report

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

Other variants

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

QC failed variants

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

Missing positions report

Chromosome	Position	Depth	Gene	Annotation	Drug related	Variant
Pf3D7_07_v3	404407	7	PF3D7_0709000	drug resistance	chloroquine	p.Ala220Ser
Pf3D7_07_v3	404408	7	PF3D7_0709000	drug resistance	chloroquine	p.Ala220Ser
Pf3D7_07_v3	404409	7	PF3D7_0709000	drug resistance	chloroquine	p.Ala220Ser
Pf3D7_07_v3	405361	7	PF3D7_0709000	drug resistance	chloroquine	p.Asn326Ser
Pf3D7_07_v3	405362	7	PF3D7_0709000	drug resistance	chloroquine	p.Asn326Ser
Pf3D7_07_v3	405363	7	PF3D7_0709000	drug resistance	chloroquine	p.Asn326Ser
Pf3D7_13_v3	1724975	7	PF3D7_1343700	drug resistance	artemisinin	p.Ala675Val

RESISTANCE REPORT OTHER VARIANTS QC FAIL VARIANTS MISSING POSITIONS REPORT

Resistance variants report

Gene	Mutations
DHFR-TS	p.Asn51Ile p.Cys59Arg p.Ser108Asn p.Ile164Leu VIEW IN IGV
MDR1	p.Tyr184Phe VIEW IN IGV
CRT	p.Lys76Thr p.Gln271Glu p.Ile356Thr p.Arg371Ile VIEW IN IGV
PPPK-DHPS	p.Ser436Ala p.Ala437Gly VIEW IN IGV

Other variants

Gene	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 VIEW IN IGV
CARL	c.-106_-105delAT c.1806G>T p.Lys903Glu c.2804_2809delATAATA p.Glu956Lys VIEW IN IGV
PI4K	c.-84C>A p.His24Leu p.Val100Ala c.2646_2649delCAACinsTAAT c.3147T>C VIEW IN IGV
MDR1	p.Asp651Asn VIEW IN IGV
CRT	p.MetAsn74IleAsp p.Asn75Lys VIEW IN IGV
PF3D7_0813000	p.Ser413Asn c.-51C>A VIEW IN IGV
PF3D7_1025000	p.Gln932Glu c.2724C>G p.Phe486Ser c.1383A>G c.1383A>G c.-145_-144delAT VIEW IN IGV
PF3D7_1036800	p.Thr459Ile VIEW IN IGV
PF3D7_1138700	p.Ser1721Ala p.Ser633Asn p.Glu497Gln p.Glu336Gln VIEW IN IGV
PF3D7_1204400	c.-162_-161delAT VIEW IN IGV
ATP4	p.Gly1128Arg c.669C>A c.-98_-91delATCTATAT VIEW IN IGV
PRS	c.1134A>G p.Val36Ile c.-62G>A VIEW IN IGV
AP2-MU	c.699_701delTAA VIEW IN IGV
PF3D7_1246300	c.1041T>C VIEW IN IGV
PF3D7_1251200	c.636A>G VIEW IN IGV
K13	c.421_426dupAATAAT c.-148C>A VIEW IN IGV
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 VIEW IN IGV

QC failed variants

Gene	Mutations
UBP1	VIEW IN IGV
DHFR-TS	VIEW IN IGV
PI4K	VIEW IN IGV
MDR1	VIEW IN IGV
CRT	VIEW IN IGV
PPPK-DHPS	VIEW IN IGV
PF3D7_0813000	VIEW IN IGV
PF3D7_1025000	VIEW IN IGV
PF3D7_1036800	VIEW IN IGV
PF3D7_1138700	VIEW IN IGV
AP2-MU	VIEW IN IGV
PF3D7_1246300	VIEW IN IGV
PF3D7_1251200	VIEW IN IGV
PF3D7_1318100	VIEW IN IGV
RAB11a	VIEW IN IGV
K13	VIEW IN IGV
MCA2	VIEW IN IGV
ARPS10	VIEW IN IGV

Missing positions report

Gene	Mutations
	VIEW IN IGV

BACK

Estimated Region of Origin

Southeast Asia - 90.0%

BACK

Est Moi

moi	Haplotype counts	Software	Software version
4	1: 6 2: 24 3: 7 4: 6 5: 2	pymoi	0.1.1

BACK

Coverage report

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

BACK

Species

Plasmodium falciparum

Species	Prediction
Plasmodium falciparum	99.76 %

BACK

Welcome to the results screen

RESULT ID: cefa3f2e-d334-4fa5-91ac-920f39cc11a0

FASTQ FILE NAME: Example file

Species view

Species

Genomic variants

Genomic variants

Sample location

Estimated Region of Origin

Tools used

Est moi.

Coverage Report

Coverage report

IGV

IGV section

RESULT ID

SPECIES

GENOMIC VARIANTS

ESTIMATED ORIGIN OF REGION

EST MOI

COVERAGE REPORT

SHOW MORE INFO

RESULT ID: cefa3f2e-d334-4fa5-91ac-920f39cc11a0

Species

Genomic variants

Estimated Region of Origin

Est Moi

Coverage report

Species