Welcome to the results screen

Here you can view your analysis

FASTQ FILE NAME: ERR1008804_1.fastq.gz

Species view

What species is your sample at 99% accuracy

Species	ANI	Abundance	Accession
Plasmodium falciparum	99.8 %	35.68	Plasmodium_falciparum

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.Asn86Tyr (1.00) , MDR1 p.Tyr184Phe (1.00) , CRT p.Met74Ile (1.00) , CRT p.Lys76Thr (1.00) , CRT p.Ala220Ser (1.00) , CRT p.Gln271Glu (1.00)
Mefloquine
Pyrimethamine
Sulfadoxine	PPPK-DHPS p.Ala437Gly (0.97)
Artemisinin

Other variants

Chromosome:	Genome Position	Locus Tag	Gene Name	Change	Estimated fraction
Pf3D7_01_v3	190616	PF3D7_0104300	UBP1	c.348A>G	1.0
Pf3D7_01_v3	190739	PF3D7_0104300	UBP1	p.Asn157Lys	1.0
Pf3D7_01_v3	190967	PF3D7_0104300	UBP1	c.699_700insAATAGTATTAATAATAGTATTAAT	0.57
Pf3D7_01_v3	191432	PF3D7_0104300	UBP1	c.1162_1164dupGAT	0.83
Pf3D7_01_v3	192111	PF3D7_0104300	UBP1	p.Tyr615His	1.0
Pf3D7_01_v3	193667	PF3D7_0104300	UBP1	p.Arg1133Ser	0.95
Pf3D7_01_v3	194117	PF3D7_0104300	UBP1	c.3849T>C	1.0
Pf3D7_01_v3	196010	PF3D7_0104300	UBP1	p.Lys1914Asn	1.0
Pf3D7_01_v3	196011	PF3D7_0104300	UBP1	p.Glu1915Lys	1.0
Pf3D7_01_v3	196981	PF3D7_0104300	UBP1	p.Arg2238Lys	0.98
Pf3D7_01_v3	199865	PF3D7_0104300	UBP1	c.9365_9391delGTATGAATCATGCAAACCGTGTGAGTC	0.53
Pf3D7_01_v3	380532	PF3D7_0109800	PF3D7_0109800	c.-165A>G	1.0
Pf3D7_01_v3	381402	PF3D7_0109800	PF3D7_0109800	c.704_706dupATA	0.94
Pf3D7_03_v3	922867	PF3D7_0321900	CARL	c.-106_-105delAT	0.95
Pf3D7_03_v3	925808	PF3D7_0321900	CARL	p.Lys903Glu	1.0
Pf3D7_04_v3	748516	PF3D7_0417200	DHFR-TS	c.429T>C	0.98
Pf3D7_05_v3	410338	PF3D7_0509800	PI4K	p.His24Leu	1.0
Pf3D7_05_v3	412895	PF3D7_0509800	PI4K	c.2628C>T	0.76
Pf3D7_05_v3	412896	PF3D7_0509800	PI4K	p.Asn877Asp	0.76
Pf3D7_05_v3	413426	PF3D7_0509800	PI4K	c.3159C>T	0.97
Pf3D7_05_v3	413958	PF3D7_0509800	PI4K	c.3689_3691dupATA	1.0
Pf3D7_05_v3	415296	PF3D7_0509800	PI4K	c.4668T>C	1.0
Pf3D7_05_v3	959837	PF3D7_0523000	MDR1	p.Asp650Asn	0.94
Pf3D7_05_v3	959843	PF3D7_0523000	MDR1	p.Asn652Asp	0.94
Pf3D7_05_v3	960046	PF3D7_0523000	MDR1	c.2157C>T	1.0
Pf3D7_07_v3	894384	PF3D7_0720700	PF3D7_0720700	c.2175C>G	1.0
Pf3D7_07_v3	895180	PF3D7_0720700	PF3D7_0720700	p.Asn991Asp	1.0
Pf3D7_07_v3	896099	PF3D7_0720700	PF3D7_0720700	c.3890_3891insAAACAATGT	0.78
Pf3D7_07_v3	897236	PF3D7_0720700	PF3D7_0720700	c.5028_5036delTGTAAAAAG	1.0
Pf3D7_07_v3	898242	PF3D7_0720700	PF3D7_0720700	c.6033C>A	1.0
Pf3D7_08_v3	548068	PF3D7_0810800	PPPK-DHPS	c.-131_-130delAT	1.0
Pf3D7_08_v3	548801	PF3D7_0810800	PPPK-DHPS	c.426G>A	1.0
Pf3D7_08_v3	643648	PF3D7_0813000	PF3D7_0813000	c.1229_1237dupATAATATGA	0.74
Pf3D7_08_v3	644383	PF3D7_0813000	PF3D7_0813000	c.491_502delGAGATAAAGATA	1.0
Pf3D7_10_v3	1046204	PF3D7_1025000	PF3D7_1025000	p.Arg859Lys	1.0
Pf3D7_10_v3	1046830	PF3D7_1025000	PF3D7_1025000	c.1950A>T	0.95
Pf3D7_10_v3	1047084	PF3D7_1025000	PF3D7_1025000	p.Asn566Asp	1.0
Pf3D7_10_v3	1047087	PF3D7_1025000	PF3D7_1025000	p.Asn565Asp	1.0
Pf3D7_10_v3	1047093	PF3D7_1025000	PF3D7_1025000	p.Tyr563Asp	1.0
Pf3D7_10_v3	1047095	PF3D7_1025000	PF3D7_1025000	p.Thr562Glu	1.0
Pf3D7_10_v3	1047108	PF3D7_1025000	PF3D7_1025000	p.Asn558Asp	1.0
Pf3D7_10_v3	1047111	PF3D7_1025000	PF3D7_1025000	p.AsnAsn556LysTyr	1.0
Pf3D7_10_v3	1047113	PF3D7_1025000	PF3D7_1025000	p.Asn556Thr	1.0
Pf3D7_10_v3	1047117	PF3D7_1025000	PF3D7_1025000	p.Asp555Asn	1.0
Pf3D7_10_v3	1047120	PF3D7_1025000	PF3D7_1025000	p.Tyr554Asn	1.0
Pf3D7_10_v3	1047122	PF3D7_1025000	PF3D7_1025000	p.Thr553Lys	1.0
Pf3D7_10_v3	1047135	PF3D7_1025000	PF3D7_1025000	p.Asn549Asp	1.0
Pf3D7_10_v3	1047138	PF3D7_1025000	PF3D7_1025000	p.AsnAsn547LysTyr	1.0
Pf3D7_10_v3	1047140	PF3D7_1025000	PF3D7_1025000	p.Asn547Thr	1.0
Pf3D7_10_v3	1047143	PF3D7_1025000	PF3D7_1025000	c.1631_1636delCATATG	1.0
Pf3D7_10_v3	1047323	PF3D7_1025000	PF3D7_1025000	p.Phe486Ser	0.98
Pf3D7_10_v3	1047779	PF3D7_1025000	PF3D7_1025000	p.Gly334Glu	1.0
Pf3D7_10_v3	1449646	PF3D7_1036800	PF3D7_1036800	p.Thr459Ile	1.0
Pf3D7_10_v3	1451029	PF3D7_1036800	PF3D7_1036800	p.Arg104Lys	1.0
Pf3D7_11_v3	1526106	PF3D7_1138700	PF3D7_1138700	p.Ser1721Ala	1.0
Pf3D7_11_v3	1528120	PF3D7_1138700	PF3D7_1138700	p.Glu1049Asp	0.96
Pf3D7_11_v3	1529369	PF3D7_1138700	PF3D7_1138700	p.Ser633Asn	1.0
Pf3D7_11_v3	1529778	PF3D7_1138700	PF3D7_1138700	p.Glu497Gln	1.0
Pf3D7_11_v3	1529908	PF3D7_1138700	PF3D7_1138700	c.1359T>C	1.0
Pf3D7_12_v3	529418	PF3D7_1211900	ATP4	p.Gly1128Arg	1.0
Pf3D7_12_v3	529559	PF3D7_1211900	ATP4	p.Gln1081Lys	1.0
Pf3D7_12_v3	532887	PF3D7_1211900	ATP4	c.-88A>C	0.98
Pf3D7_12_v3	532889	PF3D7_1211900	ATP4	c.-90C>A	0.98
Pf3D7_12_v3	592234	PF3D7_1213800	PRS	c.201G>A	1.0
Pf3D7_12_v3	592496	PF3D7_1213800	PRS	c.-62G>A	1.0
Pf3D7_12_v3	592610	PF3D7_1213800	PRS	c.-196_-177delAATATATATATATATATATA	0.95
Pf3D7_12_v3	1927229	PF3D7_1246300	PF3D7_1246300	c.1041T>C	1.0
Pf3D7_12_v3	2092045	PF3D7_1251200	PF3D7_1251200	c.-42_-41insATATAT	1.0
Pf3D7_12_v3	2092969	PF3D7_1251200	PF3D7_1251200	p.Ser183Gly	1.0
Pf3D7_12_v3	2093058	PF3D7_1251200	PF3D7_1251200	c.636A>G	1.0
Pf3D7_13_v3	1726432	PF3D7_1343700	K13	p.Lys189Thr	1.0
Pf3D7_13_v3	1727052	PF3D7_1343700	K13	c.-55A>T	0.93
Pf3D7_13_v3	1727056	PF3D7_1343700	K13	c.-59A>T	0.93
Pf3D7_13_v3	1727071	PF3D7_1343700	K13	c.-104_-75delAATATATATATATATATATATATATATATA	0.93
Pf3D7_14_v3	1550691	PF3D7_1438400	MCA2	p.Asp226Glu	1.0
Pf3D7_14_v3	1550916	PF3D7_1438400	MCA2	c.904_906delAAT	1.0
Pf3D7_14_v3	1553197	PF3D7_1438400	MCA2	p.Glu1062Gln	1.0
Pf3D7_14_v3	1553266	PF3D7_1438400	MCA2	p.Asn1085Asp	1.0
Pf3D7_14_v3	1553649	PF3D7_1438400	MCA2	c.3636C>T	1.0
Pf3D7_14_v3	1553661	PF3D7_1438400	MCA2	c.3648T>C	1.0
Pf3D7_14_v3	1553697	PF3D7_1438400	MCA2	c.3684C>T	1.0
Pf3D7_14_v3	1554029	PF3D7_1438400	MCA2	p.Glu1339Ala	1.0
Pf3D7_14_v3	1554098	PF3D7_1438400	MCA2	p.Thr1362Ile	1.0
Pf3D7_14_v3	1554318	PF3D7_1438400	MCA2	c.4305G>A	1.0
Pf3D7_14_v3	2090784	PF3D7_1451100	eEF2	c.-118_-117insAT	0.75
Pf3D7_14_v3	2480289	PF3D7_1460900	ARPS10	c.-151T>A	1.0

QC failed variants

Chromosome:	Genome Position	Locus Tag	Gene Name	Change	Estimated fraction
Pf3D7_01_v3	191090	PF3D7_0104300	UBP1	p.Asn274Lys	0.23
Pf3D7_01_v3	192530	PF3D7_0104300	UBP1	p.Asn754Lys	1.0
Pf3D7_01_v3	192533	PF3D7_0104300	UBP1	c.2265A>G	1.0
Pf3D7_01_v3	192633	PF3D7_0104300	UBP1	p.Asn789Asp	1.0
Pf3D7_01_v3	192640	PF3D7_0104300	UBP1	c.2373_2405delCGATGATGATGACGATGACAATGATGATGATGA	1.0
Pf3D7_04_v3	747914	PF3D7_0417200	DHFR-TS	c.-174C>A	0.17
Pf3D7_04_v3	747993	PF3D7_0417200	DHFR-TS	c.-95C>A	0.19
Pf3D7_04_v3	747997	PF3D7_0417200	DHFR-TS	c.-91C>A	0.15
Pf3D7_05_v3	410075	PF3D7_0509800	PI4K	c.-193C>A	0.15
Pf3D7_05_v3	410184	PF3D7_0509800	PI4K	c.-84C>A	0.16
Pf3D7_05_v3	410271	PF3D7_0509800	PI4K	p.Glu2*	0.1
Pf3D7_05_v3	410566	PF3D7_0509800	PI4K	p.Val100Ala	1.0
Pf3D7_05_v3	410608	PF3D7_0509800	PI4K	p.Gly114Asp	1.0
Pf3D7_05_v3	410611	PF3D7_0509800	PI4K	p.Asp115Gly	1.0
Pf3D7_05_v3	410638	PF3D7_0509800	PI4K	p.Gly124Asp	1.0
Pf3D7_05_v3	410644	PF3D7_0509800	PI4K	p.Asp126Gly	1.0
Pf3D7_05_v3	410656	PF3D7_0509800	PI4K	p.Asp130Gly	1.0
Pf3D7_05_v3	410668	PF3D7_0509800	PI4K	p.Asp134Gly	1.0
Pf3D7_05_v3	412890	PF3D7_0509800	PI4K	p.Asp875Asn	0.64
Pf3D7_07_v3	403519	PF3D7_0709000	CRT	p.Leu41Ile	0.2
Pf3D7_07_v3	403532	PF3D7_0709000	CRT	p.Ala45Asp	0.17
Pf3D7_07_v3	403546	PF3D7_0709000	CRT	p.Leu50Ile	0.13
Pf3D7_07_v3	403621	PF3D7_0709000	CRT	p.Asn75Glu	1.0
Pf3D7_07_v3	404032	PF3D7_0709000	CRT	p.Thr152Asn	0.29
Pf3D7_07_v3	404570	PF3D7_0709000	CRT	c.668C>A	0.17
Pf3D7_07_v3	405838	PF3D7_0709000	CRT	p.Arg371Ile	1.0
Pf3D7_07_v3	892492	PF3D7_0720700	PF3D7_0720700	c.285-2A>G	0.67
Pf3D7_07_v3	892493	PF3D7_0720700	PF3D7_0720700	c.285-1G>A	0.67
Pf3D7_07_v3	892495	PF3D7_0720700	PF3D7_0720700	c.286C>T	0.67
Pf3D7_07_v3	895153	PF3D7_0720700	PF3D7_0720700	p.Asp982Asn	0.2
Pf3D7_07_v3	896100	PF3D7_0720700	PF3D7_0720700	c.3891G>A	0.1
Pf3D7_08_v3	644936	PF3D7_0813000	PF3D7_0813000	c.-51C>A	1.0
Pf3D7_08_v3	645031	PF3D7_0813000	PF3D7_0813000	c.-147_-146insT	1.0
Pf3D7_10_v3	1049857	PF3D7_1025000	PF3D7_1025000	c.-97G>A	0.22
Pf3D7_10_v3	1049903	PF3D7_1025000	PF3D7_1025000	c.-145_-144delAT	1.0
Pf3D7_10_v3	1451758	PF3D7_1036800	PF3D7_1036800	c.-112G>T	0.14
Pf3D7_10_v3	1451781	PF3D7_1036800	PF3D7_1036800	c.-135C>A	0.29
Pf3D7_10_v3	1451794	PF3D7_1036800	PF3D7_1036800	c.-148C>T	0.8
Pf3D7_12_v3	209707	PF3D7_1204400	PF3D7_1204400	p.Cys166Phe	0.2
Pf3D7_12_v3	1925464	PF3D7_1246300	PF3D7_1246300	c.-178C>A	0.11
Pf3D7_12_v3	1925484	PF3D7_1246300	PF3D7_1246300	c.-158G>A	1.0
Pf3D7_12_v3	1925560	PF3D7_1246300	PF3D7_1246300	c.-81_-78delTATA	0.29
Pf3D7_12_v3	2091948	PF3D7_1251200	PF3D7_1251200	c.-139C>T	0.16
Pf3D7_12_v3	2091959	PF3D7_1251200	PF3D7_1251200	c.-128C>T	0.22
Pf3D7_12_v3	2092303	PF3D7_1251200	PF3D7_1251200	p.Cys25*	0.12
Pf3D7_12_v3	2092314	PF3D7_1251200	PF3D7_1251200	p.Thr29Asn	0.19
Pf3D7_12_v3	2092341	PF3D7_1251200	PF3D7_1251200	p.Ala38Asp	0.14
Pf3D7_12_v3	2092353	PF3D7_1251200	PF3D7_1251200	c.125C>A	0.12
Pf3D7_13_v3	749141	PF3D7_1318100	PF3D7_1318100	c.-170A>G	0.11
Pf3D7_13_v3	846960	PF3D7_1320600	RAB11a	c.-130G>T	0.14
Pf3D7_13_v3	847089	PF3D7_1320600	RAB11a	c.-1G>T	0.22
Pf3D7_13_v3	847120	PF3D7_1320600	RAB11a	p.Leu11Met	0.22
Pf3D7_13_v3	847305	PF3D7_1320600	RAB11a	c.43G>T	0.13
Pf3D7_14_v3	1548768	PF3D7_1438400	MCA2	c.-150C>T	0.25
Pf3D7_14_v3	1548803	PF3D7_1438400	MCA2	c.-115C>A	0.31
Pf3D7_14_v3	1550410	PF3D7_1438400	MCA2	p.Met133Val	0.31
Pf3D7_14_v3	1550437	PF3D7_1438400	MCA2	p.Met142Val	0.31
Pf3D7_14_v3	1550446	PF3D7_1438400	MCA2	p.Val145Met	0.31
Pf3D7_14_v3	1550472	PF3D7_1438400	MCA2	c.451_459dupGTGAATAAT	0.29
Pf3D7_14_v3	1550473	PF3D7_1438400	MCA2	p.Met154Val	0.13
Pf3D7_14_v3	1550491	PF3D7_1438400	MCA2	p.Val160Met	0.13
Pf3D7_14_v3	1550500	PF3D7_1438400	MCA2	p.Met163Val	0.13
Pf3D7_14_v3	1551744	PF3D7_1438400	MCA2	c.1731A>T	0.22
Pf3D7_14_v3	1551755	PF3D7_1438400	MCA2	c.1743_1745delAAA	0.22
Pf3D7_14_v3	1553546	PF3D7_1438400	MCA2	p.Ala1178Asp	0.11
Pf3D7_14_v3	1554043	PF3D7_1438400	MCA2	p.Tyr1344Lys	1.0
Pf3D7_14_v3	1556509	PF3D7_1438400	MCA2	p.Gly1997Glu	0.43

RESISTANCE REPORT OTHER VARIANTS MISSING POSITIONS

QC FAIL VARIANTS

Resistance variants report

Gene	Mutations
MDR1	p.Asn86Tyr p.Tyr184Phe VIEW IN IGV
CRT	p.Met74Ile p.Lys76Thr p.Ala220Ser p.Gln271Glu VIEW IN IGV
PPPK-DHPS	p.Ala437Gly VIEW IN IGV

Other variants

([{'chrom': 'Pf3D7_01_v3', 'pos': 190616, 'ref': 'A', 'alt': 'G', 'depth': 37, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 21, 'reverse_reads': 16, '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', 'sequence_hgvs': 'Pf3D7_01_v3:g.190616A>G', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 190739, 'ref': 'C', 'alt': 'A', 'depth': 40, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 22, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'change': 'p.Asn157Lys', 'nucleotide_change': 'c.471C>A', 'protein_change': 'p.Asn157Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'missense_variant', 'nucleotide_change': 'c.471C>A', 'protein_change': 'p.Asn157Lys', 'sequence_hgvs': 'Pf3D7_01_v3:g.190739C>A', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 190967, 'ref': 'T', 'alt': 'TAATAGTATTAATAATAGTATTAAT', 'depth': 30, 'freq': 0.57, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'conservative_inframe_insertion', 'change': 'c.699_700insAATAGTATTAATAATAGTATTAAT', 'nucleotide_change': 'c.699_700insAATAGTATTAATAATAGTATTAAT', 'protein_change': 'p.Asn233_Tyr234insAsnSerIleAsnAsnSerIleAsn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'conservative_inframe_insertion', 'nucleotide_change': 'c.699_700insAATAGTATTAATAATAGTATTAAT', 'protein_change': 'p.Asn233_Tyr234insAsnSerIleAsnAsnSerIleAsn', 'sequence_hgvs': 'Pf3D7_01_v3:g.190967T>TAATAGTATTAATAATAGTATTAAT', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 191432, 'ref': 'T', 'alt': 'TGAT', 'depth': 18, 'freq': 0.83, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'conservative_inframe_insertion', 'change': 'c.1162_1164dupGAT', 'nucleotide_change': 'c.1162_1164dupGAT', 'protein_change': 'p.Asp388dup', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'conservative_inframe_insertion', 'nucleotide_change': 'c.1162_1164dupGAT', 'protein_change': 'p.Asp388dup', 'sequence_hgvs': 'Pf3D7_01_v3:g.191432T>TGAT', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 192111, 'ref': 'T', 'alt': 'C', 'depth': 46, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 23, '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', 'sequence_hgvs': 'Pf3D7_01_v3:g.192111T>C', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 193667, 'ref': 'G', 'alt': 'C', 'depth': 42, 'freq': 0.95, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 20, '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', 'sequence_hgvs': 'Pf3D7_01_v3:g.193667G>C', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 194117, 'ref': 'T', 'alt': 'C', 'depth': 24, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 17, 'reverse_reads': 7, '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', 'sequence_hgvs': 'Pf3D7_01_v3:g.194117T>C', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 196010, 'ref': 'A', 'alt': 'C', 'depth': 35, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 22, 'reverse_reads': 13, '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', 'sequence_hgvs': 'Pf3D7_01_v3:g.196010A>C', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 196011, 'ref': 'G', 'alt': 'A', 'depth': 35, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 22, 'reverse_reads': 13, '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', 'sequence_hgvs': 'Pf3D7_01_v3:g.196011G>A', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 196981, 'ref': 'G', 'alt': 'A', 'depth': 49, 'freq': 0.98, 'sv': False, 'filter': 'pass', 'forward_reads': 25, 'reverse_reads': 23, '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', 'sequence_hgvs': 'Pf3D7_01_v3:g.196981G>A', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 199865, 'ref': 'CGTATGAATCATGCAAACCGTGTGAGTC', 'alt': 'C', 'depth': 30, 'freq': 0.53, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'change': 'c.9365_9391delGTATGAATCATGCAAACCGTGTGAGTC', 'nucleotide_change': 'c.9365_9391delGTATGAATCATGCAAACCGTGTGAGTC', 'protein_change': 'p.Arg3122_Ser3130del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0104300', 'feature_id': 'transcript:PF3D7_0104300', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.9365_9391delGTATGAATCATGCAAACCGTGTGAGTC', 'protein_change': 'p.Arg3122_Ser3130del', 'sequence_hgvs': 'Pf3D7_01_v3:g.199865CGTATGAATCATGCAAACCGTGTGAGTC>C', 'annotation': [], 'gene': 'UBP1'}], 'gene': 'UBP1'}, {'chrom': 'Pf3D7_01_v3', 'pos': 380532, 'ref': 'A', 'alt': 'G', 'depth': 32, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 19, 'reverse_reads': 13, 'sv_len': None, 'gene_id': 'PF3D7_0109800', 'feature_id': 'transcript:PF3D7_0109800', 'type': 'upstream_gene_variant', 'change': 'c.-165A>G', 'nucleotide_change': 'c.-165A>G', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0109800', 'feature_id': 'transcript:PF3D7_0109800', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-165A>G', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_01_v3:g.380532A>G', 'annotation': [], 'gene': 'PF3D7_0109800'}], 'gene': 'PF3D7_0109800'}, {'chrom': 'Pf3D7_01_v3', 'pos': 381402, 'ref': 'A', 'alt': 'AATA', 'depth': 34, 'freq': 0.94, 'sv': False, 'filter': 'pass', 'forward_reads': 16, 'reverse_reads': 16, 'sv_len': None, 'gene_id': 'PF3D7_0109800', 'feature_id': 'transcript:PF3D7_0109800', 'type': 'disruptive_inframe_insertion', 'change': 'c.704_706dupATA', 'nucleotide_change': 'c.704_706dupATA', 'protein_change': 'p.Asn235dup', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0109800', 'feature_id': 'transcript:PF3D7_0109800', 'type': 'disruptive_inframe_insertion', 'nucleotide_change': 'c.704_706dupATA', 'protein_change': 'p.Asn235dup', 'sequence_hgvs': 'Pf3D7_01_v3:g.381402A>AATA', 'annotation': [], 'gene': 'PF3D7_0109800'}], 'gene': 'PF3D7_0109800'}, {'chrom': 'Pf3D7_03_v3', 'pos': 922867, 'ref': 'CAT', 'alt': 'C', 'depth': 21, 'freq': 0.95, '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': '', 'sequence_hgvs': 'Pf3D7_03_v3:g.922867CAT>C', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_03_v3', 'pos': 925808, 'ref': 'A', 'alt': 'G', 'depth': 35, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 16, 'reverse_reads': 19, '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', 'sequence_hgvs': 'Pf3D7_03_v3:g.925808A>G', 'annotation': [], 'gene': 'CARL'}], 'gene': 'CARL'}, {'chrom': 'Pf3D7_04_v3', 'pos': 748516, 'ref': 'T', 'alt': 'C', 'depth': 42, 'freq': 0.98, 'sv': False, 'filter': 'pass', 'forward_reads': 25, 'reverse_reads': 16, 'sv_len': None, 'gene_id': 'PF3D7_0417200', 'feature_id': 'transcript:PF3D7_0417200', 'type': 'synonymous_variant', 'change': 'c.429T>C', 'nucleotide_change': 'c.429T>C', 'protein_change': 'p.Ile143Ile', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0417200', 'feature_id': 'transcript:PF3D7_0417200', 'type': 'synonymous_variant', 'nucleotide_change': 'c.429T>C', 'protein_change': 'p.Ile143Ile', 'sequence_hgvs': 'Pf3D7_04_v3:g.748516T>C', 'annotation': [], 'gene': 'DHFR-TS'}], 'gene': 'DHFR-TS'}, {'chrom': 'Pf3D7_05_v3', 'pos': 410338, 'ref': 'A', 'alt': 'T', 'depth': 12, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 6, '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', 'sequence_hgvs': 'Pf3D7_05_v3:g.410338A>T', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 412895, 'ref': 'C', 'alt': 'T', 'depth': 17, 'freq': 0.76, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 7, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'change': 'c.2628C>T', 'nucleotide_change': 'c.2628C>T', 'protein_change': 'p.Asn876Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.2628C>T', 'protein_change': 'p.Asn876Asn', 'sequence_hgvs': 'Pf3D7_05_v3:g.412895C>T', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 412896, 'ref': 'A', 'alt': 'G', 'depth': 17, 'freq': 0.76, 'sv': False, 'filter': 'pass', 'forward_reads': 6, 'reverse_reads': 7, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'change': 'p.Asn877Asp', 'nucleotide_change': 'c.2629A>G', 'protein_change': 'p.Asn877Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'missense_variant', 'nucleotide_change': 'c.2629A>G', 'protein_change': 'p.Asn877Asp', 'sequence_hgvs': 'Pf3D7_05_v3:g.412896A>G', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 413426, 'ref': 'C', 'alt': 'T', 'depth': 31, 'freq': 0.97, 'sv': False, 'filter': 'pass', 'forward_reads': 19, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'change': 'c.3159C>T', 'nucleotide_change': 'c.3159C>T', 'protein_change': 'p.Asp1053Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.3159C>T', 'protein_change': 'p.Asp1053Asp', 'sequence_hgvs': 'Pf3D7_05_v3:g.413426C>T', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 413958, 'ref': 'A', 'alt': 'AATA', 'depth': 13, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 3, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'disruptive_inframe_insertion', 'change': 'c.3689_3691dupATA', 'nucleotide_change': 'c.3689_3691dupATA', 'protein_change': 'p.Asn1230dup', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'disruptive_inframe_insertion', 'nucleotide_change': 'c.3689_3691dupATA', 'protein_change': 'p.Asn1230dup', 'sequence_hgvs': 'Pf3D7_05_v3:g.413958A>AATA', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 415296, 'ref': 'T', 'alt': 'C', 'depth': 20, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'change': 'c.4668T>C', 'nucleotide_change': 'c.4668T>C', 'protein_change': 'p.Asn1556Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0509800', 'feature_id': 'transcript:PF3D7_0509800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.4668T>C', 'protein_change': 'p.Asn1556Asn', 'sequence_hgvs': 'Pf3D7_05_v3:g.415296T>C', 'annotation': [], 'gene': 'PI4K'}], 'gene': 'PI4K'}, {'chrom': 'Pf3D7_05_v3', 'pos': 959837, 'ref': 'G', 'alt': 'A', 'depth': 53, 'freq': 0.94, 'sv': False, 'filter': 'pass', 'forward_reads': 21, 'reverse_reads': 29, 'sv_len': None, 'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'missense_variant', 'change': 'p.Asp650Asn', 'nucleotide_change': 'c.1948G>A', 'protein_change': 'p.Asp650Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'missense_variant', 'nucleotide_change': 'c.1948G>A', 'protein_change': 'p.Asp650Asn', 'sequence_hgvs': 'Pf3D7_05_v3:g.959837G>A', 'annotation': [], 'gene': 'MDR1'}], 'gene': 'MDR1'}, {'chrom': 'Pf3D7_05_v3', 'pos': 959843, 'ref': 'A', 'alt': 'G', 'depth': 53, 'freq': 0.94, 'sv': False, 'filter': 'pass', 'forward_reads': 21, 'reverse_reads': 29, 'sv_len': None, 'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'missense_variant', 'change': 'p.Asn652Asp', 'nucleotide_change': 'c.1954A>G', 'protein_change': 'p.Asn652Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'missense_variant', 'nucleotide_change': 'c.1954A>G', 'protein_change': 'p.Asn652Asp', 'sequence_hgvs': 'Pf3D7_05_v3:g.959843A>G', 'annotation': [], 'gene': 'MDR1'}], 'gene': 'MDR1'}, {'chrom': 'Pf3D7_05_v3', 'pos': 960046, 'ref': 'C', 'alt': 'T', 'depth': 26, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 13, 'sv_len': None, 'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'synonymous_variant', 'change': 'c.2157C>T', 'nucleotide_change': 'c.2157C>T', 'protein_change': 'p.Asp719Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0523000', 'feature_id': 'transcript:PF3D7_0523000', 'type': 'synonymous_variant', 'nucleotide_change': 'c.2157C>T', 'protein_change': 'p.Asp719Asp', 'sequence_hgvs': 'Pf3D7_05_v3:g.960046C>T', 'annotation': [], 'gene': 'MDR1'}], 'gene': 'MDR1'}, {'chrom': 'Pf3D7_07_v3', 'pos': 894384, 'ref': 'C', 'alt': 'G', 'depth': 28, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 14, 'reverse_reads': 14, 'sv_len': None, 'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'synonymous_variant', 'change': 'c.2175C>G', 'nucleotide_change': 'c.2175C>G', 'protein_change': 'p.Leu725Leu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'synonymous_variant', 'nucleotide_change': 'c.2175C>G', 'protein_change': 'p.Leu725Leu', 'sequence_hgvs': 'Pf3D7_07_v3:g.894384C>G', 'annotation': [], 'gene': 'PF3D7_0720700'}], 'gene': 'PF3D7_0720700'}, {'chrom': 'Pf3D7_07_v3', 'pos': 895180, 'ref': 'A', 'alt': 'G', 'depth': 16, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 5, 'sv_len': None, 'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'missense_variant', 'change': 'p.Asn991Asp', 'nucleotide_change': 'c.2971A>G', 'protein_change': 'p.Asn991Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'missense_variant', 'nucleotide_change': 'c.2971A>G', 'protein_change': 'p.Asn991Asp', 'sequence_hgvs': 'Pf3D7_07_v3:g.895180A>G', 'annotation': [], 'gene': 'PF3D7_0720700'}], 'gene': 'PF3D7_0720700'}, {'chrom': 'Pf3D7_07_v3', 'pos': 896099, 'ref': 'T', 'alt': 'TAAACAATGT', 'depth': 45, 'freq': 0.78, 'sv': False, 'filter': 'pass', 'forward_reads': 17, 'reverse_reads': 18, 'sv_len': None, 'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'disruptive_inframe_insertion', 'change': 'c.3890_3891insAAACAATGT', 'nucleotide_change': 'c.3890_3891insAAACAATGT', 'protein_change': 'p.Val1297_Asn1298insAsnAsnVal', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'disruptive_inframe_insertion', 'nucleotide_change': 'c.3890_3891insAAACAATGT', 'protein_change': 'p.Val1297_Asn1298insAsnAsnVal', 'sequence_hgvs': 'Pf3D7_07_v3:g.896099T>TAAACAATGT', 'annotation': [], 'gene': 'PF3D7_0720700'}], 'gene': 'PF3D7_0720700'}, {'chrom': 'Pf3D7_07_v3', 'pos': 897236, 'ref': 'GTGTAAAAAG', 'alt': 'G', 'depth': 35, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 24, 'sv_len': None, 'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'disruptive_inframe_deletion', 'change': 'c.5028_5036delTGTAAAAAG', 'nucleotide_change': 'c.5028_5036delTGTAAAAAG', 'protein_change': 'p.Val1677_Ser1679del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.5028_5036delTGTAAAAAG', 'protein_change': 'p.Val1677_Ser1679del', 'sequence_hgvs': 'Pf3D7_07_v3:g.897236GTGTAAAAAG>G', 'annotation': [], 'gene': 'PF3D7_0720700'}], 'gene': 'PF3D7_0720700'}, {'chrom': 'Pf3D7_07_v3', 'pos': 898242, 'ref': 'C', 'alt': 'A', 'depth': 11, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'synonymous_variant', 'change': 'c.6033C>A', 'nucleotide_change': 'c.6033C>A', 'protein_change': 'p.Ser2011Ser', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0720700', 'feature_id': 'transcript:PF3D7_0720700', 'type': 'synonymous_variant', 'nucleotide_change': 'c.6033C>A', 'protein_change': 'p.Ser2011Ser', 'sequence_hgvs': 'Pf3D7_07_v3:g.898242C>A', 'annotation': [], 'gene': 'PF3D7_0720700'}], 'gene': 'PF3D7_0720700'}, {'chrom': 'Pf3D7_08_v3', 'pos': 548068, 'ref': 'AAT', 'alt': 'A', 'depth': 30, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 15, 'reverse_reads': 15, 'sv_len': None, 'gene_id': 'PF3D7_0810800', 'feature_id': 'transcript:PF3D7_0810800', 'type': 'upstream_gene_variant', 'change': 'c.-131_-130delAT', 'nucleotide_change': 'c.-131_-130delAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0810800', 'feature_id': 'transcript:PF3D7_0810800', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-131_-130delAT', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_08_v3:g.548068AAT>A', 'annotation': [], 'gene': 'PPPK-DHPS'}], 'gene': 'PPPK-DHPS'}, {'chrom': 'Pf3D7_08_v3', 'pos': 548801, 'ref': 'G', 'alt': 'A', 'depth': 27, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 17, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_0810800', 'feature_id': 'transcript:PF3D7_0810800', 'type': 'synonymous_variant', 'change': 'c.426G>A', 'nucleotide_change': 'c.426G>A', 'protein_change': 'p.Lys142Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0810800', 'feature_id': 'transcript:PF3D7_0810800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.426G>A', 'protein_change': 'p.Lys142Lys', 'sequence_hgvs': 'Pf3D7_08_v3:g.548801G>A', 'annotation': [], 'gene': 'PPPK-DHPS'}], 'gene': 'PPPK-DHPS'}, {'chrom': 'Pf3D7_08_v3', 'pos': 643648, 'ref': 'C', 'alt': 'CTCATATTAT', 'depth': 38, 'freq': 0.74, 'sv': False, 'filter': 'pass', 'forward_reads': 17, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'conservative_inframe_insertion', 'change': 'c.1229_1237dupATAATATGA', 'nucleotide_change': 'c.1229_1237dupATAATATGA', 'protein_change': 'p.Asn410_Met412dup', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'conservative_inframe_insertion', 'nucleotide_change': 'c.1229_1237dupATAATATGA', 'protein_change': 'p.Asn410_Met412dup', 'sequence_hgvs': 'Pf3D7_08_v3:g.643648C>CTCATATTAT', 'annotation': [], 'gene': 'PF3D7_0813000'}], 'gene': 'PF3D7_0813000'}, {'chrom': 'Pf3D7_08_v3', 'pos': 644383, 'ref': 'TTATCTTTATCTC', 'alt': 'T', 'depth': 9, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 4, 'sv_len': None, 'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'disruptive_inframe_deletion', 'change': 'c.491_502delGAGATAAAGATA', 'nucleotide_change': 'c.491_502delGAGATAAAGATA', 'protein_change': 'p.Arg164_Asp167del', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_0813000', 'feature_id': 'transcript:PF3D7_0813000', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.491_502delGAGATAAAGATA', 'protein_change': 'p.Arg164_Asp167del', 'sequence_hgvs': 'Pf3D7_08_v3:g.644383TTATCTTTATCTC>T', 'annotation': [], 'gene': 'PF3D7_0813000'}], 'gene': 'PF3D7_0813000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1046204, 'ref': 'C', 'alt': 'T', 'depth': 49, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 22, 'reverse_reads': 27, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Arg859Lys', 'nucleotide_change': 'c.2576G>A', 'protein_change': 'p.Arg859Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.2576G>A', 'protein_change': 'p.Arg859Lys', 'sequence_hgvs': 'Pf3D7_10_v3:g.1046204C>T', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1046830, 'ref': 'T', 'alt': 'A', 'depth': 43, 'freq': 0.95, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 21, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'change': 'c.1950A>T', 'nucleotide_change': 'c.1950A>T', 'protein_change': 'p.Ile650Ile', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1950A>T', 'protein_change': 'p.Ile650Ile', 'sequence_hgvs': 'Pf3D7_10_v3:g.1046830T>A', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047084, 'ref': 'T', 'alt': 'C', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Asn566Asp', 'nucleotide_change': 'c.1696A>G', 'protein_change': 'p.Asn566Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1696A>G', 'protein_change': 'p.Asn566Asp', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047084T>C', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047087, 'ref': 'T', 'alt': 'C', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Asn565Asp', 'nucleotide_change': 'c.1693A>G', 'protein_change': 'p.Asn565Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1693A>G', 'protein_change': 'p.Asn565Asp', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047087T>C', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047093, 'ref': 'AT', 'alt': 'CA', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Tyr563Asp', 'nucleotide_change': 'c.1686_1687delATinsTG', 'protein_change': 'p.Tyr563Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1686_1687delATinsTG', 'protein_change': 'p.Tyr563Asp', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047093AT>CA', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047095, 'ref': 'GT', 'alt': 'TC', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Thr562Glu', 'nucleotide_change': 'c.1684_1685delACinsGA', 'protein_change': 'p.Thr562Glu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1684_1685delACinsGA', 'protein_change': 'p.Thr562Glu', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047095GT>TC', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047108, 'ref': 'T', 'alt': 'C', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Asn558Asp', 'nucleotide_change': 'c.1672A>G', 'protein_change': 'p.Asn558Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1672A>G', 'protein_change': 'p.Asn558Asp', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047108T>C', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047111, 'ref': 'TA', 'alt': 'AT', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.AsnAsn556LysTyr', 'nucleotide_change': 'c.1668_1669delTAinsAT', 'protein_change': 'p.AsnAsn556LysTyr', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1668_1669delTAinsAT', 'protein_change': 'p.AsnAsn556LysTyr', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047111TA>AT', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047113, 'ref': 'T', 'alt': 'G', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Asn556Thr', 'nucleotide_change': 'c.1667A>C', 'protein_change': 'p.Asn556Thr', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1667A>C', 'protein_change': 'p.Asn556Thr', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047113T>G', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047117, 'ref': 'C', 'alt': 'T', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Asp555Asn', 'nucleotide_change': 'c.1663G>A', 'protein_change': 'p.Asp555Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1663G>A', 'protein_change': 'p.Asp555Asn', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047117C>T', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047120, 'ref': 'AT', 'alt': 'TA', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Tyr554Asn', 'nucleotide_change': 'c.1659_1660delATinsTA', 'protein_change': 'p.Tyr554Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1659_1660delATinsTA', 'protein_change': 'p.Tyr554Asn', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047120AT>TA', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047122, 'ref': 'G', 'alt': 'T', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Thr553Lys', 'nucleotide_change': 'c.1658C>A', 'protein_change': 'p.Thr553Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1658C>A', 'protein_change': 'p.Thr553Lys', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047122G>T', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047135, 'ref': 'T', 'alt': 'C', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Asn549Asp', 'nucleotide_change': 'c.1645A>G', 'protein_change': 'p.Asn549Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1645A>G', 'protein_change': 'p.Asn549Asp', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047135T>C', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047138, 'ref': 'TA', 'alt': 'AT', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.AsnAsn547LysTyr', 'nucleotide_change': 'c.1641_1642delTAinsAT', 'protein_change': 'p.AsnAsn547LysTyr', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1641_1642delTAinsAT', 'protein_change': 'p.AsnAsn547LysTyr', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047138TA>AT', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047140, 'ref': 'T', 'alt': 'G', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Asn547Thr', 'nucleotide_change': 'c.1640A>C', 'protein_change': 'p.Asn547Thr', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1640A>C', 'protein_change': 'p.Asn547Thr', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047140T>G', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047143, 'ref': 'TCATATG', 'alt': 'T', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 10, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'disruptive_inframe_deletion', 'change': 'c.1631_1636delCATATG', 'nucleotide_change': 'c.1631_1636delCATATG', 'protein_change': 'p.Thr544_Asp546delinsAsn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'disruptive_inframe_deletion', 'nucleotide_change': 'c.1631_1636delCATATG', 'protein_change': 'p.Thr544_Asp546delinsAsn', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047143TCATATG>T', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047323, 'ref': 'A', 'alt': 'G', 'depth': 48, 'freq': 0.98, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 27, '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', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047323A>G', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1047779, 'ref': 'C', 'alt': 'T', 'depth': 33, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 19, 'reverse_reads': 14, 'sv_len': None, 'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'change': 'p.Gly334Glu', 'nucleotide_change': 'c.1001G>A', 'protein_change': 'p.Gly334Glu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1025000', 'feature_id': 'transcript:PF3D7_1025000', 'type': 'missense_variant', 'nucleotide_change': 'c.1001G>A', 'protein_change': 'p.Gly334Glu', 'sequence_hgvs': 'Pf3D7_10_v3:g.1047779C>T', 'annotation': [], 'gene': 'PF3D7_1025000'}], 'gene': 'PF3D7_1025000'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1449646, 'ref': 'G', 'alt': 'A', 'depth': 39, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 21, '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', 'sequence_hgvs': 'Pf3D7_10_v3:g.1449646G>A', 'annotation': [], 'gene': 'PF3D7_1036800'}], 'gene': 'PF3D7_1036800'}, {'chrom': 'Pf3D7_10_v3', 'pos': 1451029, 'ref': 'C', 'alt': 'T', 'depth': 21, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 14, 'reverse_reads': 7, 'sv_len': None, 'gene_id': 'PF3D7_1036800', 'feature_id': 'transcript:PF3D7_1036800', 'type': 'missense_variant', 'change': 'p.Arg104Lys', 'nucleotide_change': 'c.311G>A', 'protein_change': 'p.Arg104Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1036800', 'feature_id': 'transcript:PF3D7_1036800', 'type': 'missense_variant', 'nucleotide_change': 'c.311G>A', 'protein_change': 'p.Arg104Lys', 'sequence_hgvs': 'Pf3D7_10_v3:g.1451029C>T', 'annotation': [], 'gene': 'PF3D7_1036800'}], 'gene': 'PF3D7_1036800'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1526106, 'ref': 'A', 'alt': 'C', 'depth': 35, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 18, 'reverse_reads': 17, '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', 'sequence_hgvs': 'Pf3D7_11_v3:g.1526106A>C', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1528120, 'ref': 'T', 'alt': 'A', 'depth': 27, 'freq': 0.96, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 15, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'change': 'p.Glu1049Asp', 'nucleotide_change': 'c.3147A>T', 'protein_change': 'p.Glu1049Asp', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'missense_variant', 'nucleotide_change': 'c.3147A>T', 'protein_change': 'p.Glu1049Asp', 'sequence_hgvs': 'Pf3D7_11_v3:g.1528120T>A', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1529369, 'ref': 'C', 'alt': 'T', 'depth': 21, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 13, 'reverse_reads': 8, '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', 'sequence_hgvs': 'Pf3D7_11_v3:g.1529369C>T', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1529778, 'ref': 'C', 'alt': 'G', 'depth': 41, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 21, 'reverse_reads': 20, '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', 'sequence_hgvs': 'Pf3D7_11_v3:g.1529778C>G', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_11_v3', 'pos': 1529908, 'ref': 'A', 'alt': 'G', 'depth': 31, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 14, 'reverse_reads': 17, 'sv_len': None, 'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'synonymous_variant', 'change': 'c.1359T>C', 'nucleotide_change': 'c.1359T>C', 'protein_change': 'p.Asn453Asn', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1138700', 'feature_id': 'transcript:PF3D7_1138700', 'type': 'synonymous_variant', 'nucleotide_change': 'c.1359T>C', 'protein_change': 'p.Asn453Asn', 'sequence_hgvs': 'Pf3D7_11_v3:g.1529908A>G', 'annotation': [], 'gene': 'PF3D7_1138700'}], 'gene': 'PF3D7_1138700'}, {'chrom': 'Pf3D7_12_v3', 'pos': 529418, 'ref': 'C', 'alt': 'T', 'depth': 51, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 26, 'reverse_reads': 25, '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', 'sequence_hgvs': 'Pf3D7_12_v3:g.529418C>T', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 529559, 'ref': 'G', 'alt': 'T', 'depth': 38, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 14, 'reverse_reads': 24, 'sv_len': None, 'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'missense_variant', 'change': 'p.Gln1081Lys', 'nucleotide_change': 'c.3241C>A', 'protein_change': 'p.Gln1081Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'missense_variant', 'nucleotide_change': 'c.3241C>A', 'protein_change': 'p.Gln1081Lys', 'sequence_hgvs': 'Pf3D7_12_v3:g.529559G>T', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 532887, 'ref': 'T', 'alt': 'G', 'depth': 43, 'freq': 0.98, 'sv': False, 'filter': 'pass', 'forward_reads': 26, 'reverse_reads': 16, 'sv_len': None, 'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'upstream_gene_variant', 'change': 'c.-88A>C', 'nucleotide_change': 'c.-88A>C', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-88A>C', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_12_v3:g.532887T>G', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 532889, 'ref': 'G', 'alt': 'T', 'depth': 43, 'freq': 0.98, 'sv': False, 'filter': 'pass', 'forward_reads': 26, 'reverse_reads': 16, 'sv_len': None, 'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'upstream_gene_variant', 'change': 'c.-90C>A', 'nucleotide_change': 'c.-90C>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1211900', 'feature_id': 'transcript:PF3D7_1211900', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-90C>A', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_12_v3:g.532889G>T', 'annotation': [], 'gene': 'ATP4'}], 'gene': 'ATP4'}, {'chrom': 'Pf3D7_12_v3', 'pos': 592234, 'ref': 'C', 'alt': 'T', 'depth': 44, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 24, 'sv_len': None, 'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'synonymous_variant', 'change': 'c.201G>A', 'nucleotide_change': 'c.201G>A', 'protein_change': 'p.Lys67Lys', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'synonymous_variant', 'nucleotide_change': 'c.201G>A', 'protein_change': 'p.Lys67Lys', 'sequence_hgvs': 'Pf3D7_12_v3:g.592234C>T', 'annotation': [], 'gene': 'PRS'}], 'gene': 'PRS'}, {'chrom': 'Pf3D7_12_v3', 'pos': 592496, 'ref': 'C', 'alt': 'T', 'depth': 24, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 11, 'reverse_reads': 13, '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': '', 'sequence_hgvs': 'Pf3D7_12_v3:g.592496C>T', 'annotation': [], 'gene': 'PRS'}], 'gene': 'PRS'}, {'chrom': 'Pf3D7_12_v3', 'pos': 592610, 'ref': 'ATATATATATATATATATATT', 'alt': 'A', 'depth': 20, 'freq': 0.95, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 11, 'sv_len': None, 'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'upstream_gene_variant', 'change': 'c.-196_-177delAATATATATATATATATATA', 'nucleotide_change': 'c.-196_-177delAATATATATATATATATATA', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1213800', 'feature_id': 'transcript:PF3D7_1213800', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-196_-177delAATATATATATATATATATA', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_12_v3:g.592610ATATATATATATATATATATT>A', 'annotation': [], 'gene': 'PRS'}], 'gene': 'PRS'}, {'chrom': 'Pf3D7_12_v3', 'pos': 1927229, 'ref': 'T', 'alt': 'C', 'depth': 30, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 20, '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', 'sequence_hgvs': 'Pf3D7_12_v3:g.1927229T>C', 'annotation': [], 'gene': 'PF3D7_1246300'}], 'gene': 'PF3D7_1246300'}, {'chrom': 'Pf3D7_12_v3', 'pos': 2092045, 'ref': 'A', 'alt': 'AATATAT', 'depth': 10, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 4, 'reverse_reads': 6, 'sv_len': None, 'gene_id': 'PF3D7_1251200', 'feature_id': 'transcript:PF3D7_1251200', 'type': 'upstream_gene_variant', 'change': 'c.-42_-41insATATAT', 'nucleotide_change': 'c.-42_-41insATATAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1251200', 'feature_id': 'transcript:PF3D7_1251200', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-42_-41insATATAT', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_12_v3:g.2092045A>AATATAT', 'annotation': [], 'gene': 'PF3D7_1251200'}], 'gene': 'PF3D7_1251200'}, {'chrom': 'Pf3D7_12_v3', 'pos': 2092969, 'ref': 'A', 'alt': 'G', 'depth': 17, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 7, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_1251200', 'feature_id': 'transcript:PF3D7_1251200', 'type': 'missense_variant', 'change': 'p.Ser183Gly', 'nucleotide_change': 'c.547A>G', 'protein_change': 'p.Ser183Gly', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1251200', 'feature_id': 'transcript:PF3D7_1251200', 'type': 'missense_variant', 'nucleotide_change': 'c.547A>G', 'protein_change': 'p.Ser183Gly', 'sequence_hgvs': 'Pf3D7_12_v3:g.2092969A>G', 'annotation': [], 'gene': 'PF3D7_1251200'}], 'gene': 'PF3D7_1251200'}, {'chrom': 'Pf3D7_12_v3', 'pos': 2093058, 'ref': 'A', 'alt': 'G', 'depth': 17, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 7, 'reverse_reads': 10, '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', 'sequence_hgvs': 'Pf3D7_12_v3:g.2093058A>G', 'annotation': [], 'gene': 'PF3D7_1251200'}], 'gene': 'PF3D7_1251200'}, {'chrom': 'Pf3D7_13_v3', 'pos': 1726432, 'ref': 'T', 'alt': 'G', 'depth': 49, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 21, 'reverse_reads': 28, 'sv_len': None, 'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'missense_variant', 'change': 'p.Lys189Thr', 'nucleotide_change': 'c.566A>C', 'protein_change': 'p.Lys189Thr', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'missense_variant', 'nucleotide_change': 'c.566A>C', 'protein_change': 'p.Lys189Thr', 'sequence_hgvs': 'Pf3D7_13_v3:g.1726432T>G', 'annotation': [], 'gene': 'K13'}], 'gene': 'K13'}, {'chrom': 'Pf3D7_13_v3', 'pos': 1727052, 'ref': 'T', 'alt': 'A', 'depth': 15, 'freq': 0.93, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'change': 'c.-55A>T', 'nucleotide_change': 'c.-55A>T', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-55A>T', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_13_v3:g.1727052T>A', 'annotation': [], 'gene': 'K13'}], 'gene': 'K13'}, {'chrom': 'Pf3D7_13_v3', 'pos': 1727056, 'ref': 'T', 'alt': 'A', 'depth': 15, 'freq': 0.93, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'change': 'c.-59A>T', 'nucleotide_change': 'c.-59A>T', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-59A>T', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_13_v3:g.1727056T>A', 'annotation': [], 'gene': 'K13'}], 'gene': 'K13'}, {'chrom': 'Pf3D7_13_v3', 'pos': 1727071, 'ref': 'ATATATATATATATATATATATATATATATT', 'alt': 'A', 'depth': 15, 'freq': 0.93, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 9, 'sv_len': None, 'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'change': 'c.-104_-75delAATATATATATATATATATATATATATATA', 'nucleotide_change': 'c.-104_-75delAATATATATATATATATATATATATATATA', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1343700', 'feature_id': 'transcript:PF3D7_1343700', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-104_-75delAATATATATATATATATATATATATATATA', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_13_v3:g.1727071ATATATATATATATATATATATATATATATT>A', 'annotation': [], 'gene': 'K13'}], 'gene': 'K13'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550691, 'ref': 'T', 'alt': 'A', 'depth': 22, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 12, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.Asp226Glu', 'nucleotide_change': 'c.678T>A', 'protein_change': 'p.Asp226Glu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.678T>A', 'protein_change': 'p.Asp226Glu', 'sequence_hgvs': 'Pf3D7_14_v3:g.1550691T>A', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1550916, 'ref': 'TAAT', 'alt': 'T', 'depth': 43, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 22, 'reverse_reads': 21, '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', 'sequence_hgvs': 'Pf3D7_14_v3:g.1550916TAAT>T', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1553197, 'ref': 'G', 'alt': 'C', 'depth': 20, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.Glu1062Gln', 'nucleotide_change': 'c.3184G>C', 'protein_change': 'p.Glu1062Gln', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.3184G>C', 'protein_change': 'p.Glu1062Gln', 'sequence_hgvs': 'Pf3D7_14_v3:g.1553197G>C', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1553266, 'ref': 'A', 'alt': 'G', 'depth': 20, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 12, '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', 'sequence_hgvs': 'Pf3D7_14_v3:g.1553266A>G', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1553649, 'ref': 'C', 'alt': 'T', 'depth': 41, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 21, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'change': 'c.3636C>T', 'nucleotide_change': 'c.3636C>T', 'protein_change': 'p.His1212His', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'nucleotide_change': 'c.3636C>T', 'protein_change': 'p.His1212His', 'sequence_hgvs': 'Pf3D7_14_v3:g.1553649C>T', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1553661, 'ref': 'T', 'alt': 'C', 'depth': 41, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 21, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'change': 'c.3648T>C', 'nucleotide_change': 'c.3648T>C', 'protein_change': 'p.His1216His', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'nucleotide_change': 'c.3648T>C', 'protein_change': 'p.His1216His', 'sequence_hgvs': 'Pf3D7_14_v3:g.1553661T>C', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1553697, 'ref': 'C', 'alt': 'T', 'depth': 41, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 20, 'reverse_reads': 21, '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', 'sequence_hgvs': 'Pf3D7_14_v3:g.1553697C>T', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1554029, 'ref': 'A', 'alt': 'C', 'depth': 17, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.Glu1339Ala', 'nucleotide_change': 'c.4016A>C', 'protein_change': 'p.Glu1339Ala', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.4016A>C', 'protein_change': 'p.Glu1339Ala', 'sequence_hgvs': 'Pf3D7_14_v3:g.1554029A>C', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1554098, 'ref': 'C', 'alt': 'T', 'depth': 17, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 5, 'reverse_reads': 12, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'change': 'p.Thr1362Ile', 'nucleotide_change': 'c.4085C>T', 'protein_change': 'p.Thr1362Ile', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'missense_variant', 'nucleotide_change': 'c.4085C>T', 'protein_change': 'p.Thr1362Ile', 'sequence_hgvs': 'Pf3D7_14_v3:g.1554098C>T', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 1554318, 'ref': 'G', 'alt': 'A', 'depth': 33, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 17, 'reverse_reads': 16, 'sv_len': None, 'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'change': 'c.4305G>A', 'nucleotide_change': 'c.4305G>A', 'protein_change': 'p.Glu1435Glu', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1438400', 'feature_id': 'transcript:PF3D7_1438400', 'type': 'synonymous_variant', 'nucleotide_change': 'c.4305G>A', 'protein_change': 'p.Glu1435Glu', 'sequence_hgvs': 'Pf3D7_14_v3:g.1554318G>A', 'annotation': [], 'gene': 'MCA2'}], 'gene': 'MCA2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 2090784, 'ref': 'A', 'alt': 'AAT', 'depth': 24, 'freq': 0.75, 'sv': False, 'filter': 'pass', 'forward_reads': 8, 'reverse_reads': 10, 'sv_len': None, 'gene_id': 'PF3D7_1451100', 'feature_id': 'transcript:PF3D7_1451100', 'type': 'upstream_gene_variant', 'change': 'c.-118_-117insAT', 'nucleotide_change': 'c.-118_-117insAT', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1451100', 'feature_id': 'transcript:PF3D7_1451100', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-118_-117insAT', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_14_v3:g.2090784A>AAT', 'annotation': [], 'gene': 'eEF2'}], 'gene': 'eEF2'}, {'chrom': 'Pf3D7_14_v3', 'pos': 2480289, 'ref': 'T', 'alt': 'A', 'depth': 26, 'freq': 1.0, 'sv': False, 'filter': 'pass', 'forward_reads': 12, 'reverse_reads': 14, 'sv_len': None, 'gene_id': 'PF3D7_1460900', 'feature_id': 'transcript:PF3D7_1460900', 'type': 'upstream_gene_variant', 'change': 'c.-151T>A', 'nucleotide_change': 'c.-151T>A', 'protein_change': '', 'annotation': [], 'consequences': [{'gene_id': 'PF3D7_1460900', 'feature_id': 'transcript:PF3D7_1460900', 'type': 'upstream_gene_variant', 'nucleotide_change': 'c.-151T>A', 'protein_change': '', 'sequence_hgvs': 'Pf3D7_14_v3:g.2480289T>A', 'annotation': [], 'gene': 'ARPS10'}], 'gene': 'ARPS10'}], {'chrom': 'Chromosome:', 'pos': 'Genome Position', 'gene_id': 'Locus Tag', 'gene': 'Gene Name', 'change': 'Change', 'freq': 'Estimated fraction'}, 'Other variants', 'falciparum')

Gene	Mutations
UBP1	c.348A>G p.Asn157Lys c.699_700insAATAGTATTAATAATAGTATTAAT c.1162_1164dupGAT p.Tyr615His p.Arg1133Ser c.3849T>C p.Lys1914Asn p.Glu1915Lys p.Arg2238Lys c.9365_9391delGTATGAATCATGCAAACCGTGTGAGTC VIEW IN IGV
PF3D7_0109800	c.-165A>G c.704_706dupATA VIEW IN IGV
CARL	c.-106_-105delAT p.Lys903Glu VIEW IN IGV
DHFR-TS	c.429T>C VIEW IN IGV
PI4K	p.His24Leu c.2628C>T p.Asn877Asp c.3159C>T c.3689_3691dupATA c.4668T>C VIEW IN IGV
MDR1	p.Asp650Asn p.Asn652Asp c.2157C>T VIEW IN IGV
PF3D7_0720700	c.2175C>G p.Asn991Asp c.3890_3891insAAACAATGT c.5028_5036delTGTAAAAAG c.6033C>A VIEW IN IGV
PPPK-DHPS	c.-131_-130delAT c.426G>A VIEW IN IGV
PF3D7_0813000	c.1229_1237dupATAATATGA c.491_502delGAGATAAAGATA VIEW IN IGV
PF3D7_1025000	p.Arg859Lys c.1950A>T p.Asn566Asp p.Asn565Asp p.Tyr563Asp p.Thr562Glu p.Asn558Asp p.AsnAsn556LysTyr p.Asn556Thr p.Asp555Asn p.Tyr554Asn p.Thr553Lys p.Asn549Asp p.AsnAsn547LysTyr p.Asn547Thr c.1631_1636delCATATG p.Phe486Ser p.Gly334Glu VIEW IN IGV
PF3D7_1036800	p.Thr459Ile p.Arg104Lys VIEW IN IGV
PF3D7_1138700	p.Ser1721Ala p.Glu1049Asp p.Ser633Asn p.Glu497Gln c.1359T>C VIEW IN IGV
ATP4	p.Gly1128Arg p.Gln1081Lys c.-88A>C c.-90C>A VIEW IN IGV
PRS	c.201G>A c.-62G>A c.-196_-177delAATATATATATATATATATA VIEW IN IGV
PF3D7_1246300	c.1041T>C VIEW IN IGV
PF3D7_1251200	c.-42_-41insATATAT p.Ser183Gly c.636A>G VIEW IN IGV
K13	p.Lys189Thr c.-55A>T c.-59A>T c.-104_-75delAATATATATATATATATATATATATATATA VIEW IN IGV
MCA2	p.Asp226Glu c.904_906delAAT p.Glu1062Gln p.Asn1085Asp c.3636C>T c.3648T>C c.3684C>T p.Glu1339Ala p.Thr1362Ile c.4305G>A VIEW IN IGV
eEF2	c.-118_-117insAT VIEW IN IGV
ARPS10	c.-151T>A VIEW IN IGV

QC failed variants

Gene	Mutations
UBP1	VIEW IN IGV
DHFR-TS	VIEW IN IGV
PI4K	VIEW IN IGV
CRT	VIEW IN IGV
PF3D7_0720700	VIEW IN IGV
PF3D7_0813000	VIEW IN IGV
PF3D7_1025000	VIEW IN IGV
PF3D7_1036800	VIEW IN IGV
PF3D7_1204400	VIEW IN IGV
PF3D7_1246300	VIEW IN IGV
PF3D7_1251200	VIEW IN IGV
PF3D7_1318100	VIEW IN IGV
RAB11a	VIEW IN IGV
MCA2	VIEW IN IGV

Missing positions report

Gene	Mutations

Sample location

Where your sample is from

Estimated Region of Origin

Western Africa - 100.0%

Percentage of barcoding SNPs that have coverage: 100.0 %

Est Moi

The estimated multiplicity of infection for your sample

Process	Software
Software	{'taxonomic_software': 'sourmash', 'trimming': 'trimmomatic', 'mapping': 'bwa', 'variant_calling': 'freebayes-Haplotype', 'depth_calculation': 'samtools'}

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	99.92	40.0

Gene	Percentage Depth passed	Median Depth
PF3D7_0109800	100.0	38.0

Gene	Percentage Depth passed	Median Depth
CARL	100.0	33.0

Gene	Percentage Depth passed	Median Depth
DHFR-TS	100.0	43.0

Gene	Percentage Depth passed	Median Depth
PI4K	100.0	39.0

Gene	Percentage Depth passed	Median Depth
MDR1	100.0	39.0

Gene	Percentage Depth passed	Median Depth
DHODH	100.0	43.0

Gene	Percentage Depth passed	Median Depth
CRT	99.48	24.0

Gene	Percentage Depth passed	Median Depth
PF3D7_0720700	100.0	40.0

Gene	Percentage Depth passed	Median Depth
PPPK-DHPS	100.0	39.0

Gene	Percentage Depth passed	Median Depth
PF3D7_0813000	100.0	38.0

Gene	Percentage Depth passed	Median Depth
PF3D7_1025000	99.91	43.0

Gene	Percentage Depth passed	Median Depth
PF3D7_1036800	100.0	35.0

Gene	Percentage Depth passed	Median Depth
PF3D7_1113300	100.0	32.0

Gene	Percentage Depth passed	Median Depth
PF3D7_1138700	100.0	42.0

Gene	Percentage Depth passed	Median Depth
PF3D7_1204400	100.0	27.0

Gene	Percentage Depth passed	Median Depth
ATP4	100.0	45.0

Gene	Percentage Depth passed	Median Depth
PRS	100.0	40.0

Gene	Percentage Depth passed	Median Depth
AP2-MU	100.0	34.0

Gene	Percentage Depth passed	Median Depth
PF3D7_1246300	100.0	31.0

Gene	Percentage Depth passed	Median Depth
PF3D7_1251200	100.0	36.0

Gene	Percentage Depth passed	Median Depth
PF3D7_1318100	100.0	33.0

Gene	Percentage Depth passed	Median Depth
RAB11a	100.0	26.0

Gene	Percentage Depth passed	Median Depth
K13	100.0	42.0

Gene	Percentage Depth passed	Median Depth
MCA2	100.0	37.0

Gene	Percentage Depth passed	Median Depth
eEF2	100.0	43.0

Gene	Percentage Depth passed	Median Depth
ARPS10	100.0	29.0

Gene	Percentage Depth passed	Median Depth
CYTB	100.0	960.0

SEE ALL

Coverage report

Gene	Percentage depth passed	Median Depth
UBP1	99.92	40.0
PF3D7_0109800	100.0	38.0
CARL	100.0	33.0
DHFR-TS	100.0	43.0
PI4K	100.0	39.0
MDR1	100.0	39.0
DHODH	100.0	43.0
CRT	99.48	24.0
PF3D7_0720700	100.0	40.0
PPPK-DHPS	100.0	39.0
PF3D7_0813000	100.0	38.0
PF3D7_1025000	99.91	43.0
PF3D7_1036800	100.0	35.0
PF3D7_1113300	100.0	32.0
PF3D7_1138700	100.0	42.0
PF3D7_1204400	100.0	27.0
ATP4	100.0	45.0
PRS	100.0	40.0
AP2-MU	100.0	34.0
PF3D7_1246300	100.0	31.0
PF3D7_1251200	100.0	36.0
PF3D7_1318100	100.0	33.0
RAB11a	100.0	26.0
K13	100.0	42.0
MCA2	100.0	37.0
eEF2	100.0	43.0
ARPS10	100.0	29.0
CYTB	100.0	960.0

IGV

View certain areas of interest using IGV

RESULT ID

SPECIES

GENOMIC VARIANTS

ESTIMATED ORIGIN OF REGION

ANALYSIS

COVERAGE REPORT

SHOW MORE INFO

RESULT ID: 90f2cb47-60c6-41c0-a50b-a06b70dcd5f6

Identifier	Date
Err1008804	Fri May 1 08:41:38 2026

BACK

Species

Species	ANI	Abundance	Accession
Plasmodium falciparum	99.8 %	35.68	Plasmodium_falciparum

BACK

Genomic variants

Resistance report

Drug	Mutations
Chloroquine	MDR1 p.Asn86Tyr (1.00) , MDR1 p.Tyr184Phe (1.00) , CRT p.Met74Ile (1.00) , CRT p.Lys76Thr (1.00) , CRT p.Ala220Ser (1.00) , CRT p.Gln271Glu (1.00)
Mefloquine
Pyrimethamine
Sulfadoxine	PPPK-DHPS p.Ala437Gly (0.97)
Artemisinin

Other variants

Chromosome:	Genome Position	Locus Tag	Gene Name	Change	Estimated fraction
Pf3D7_01_v3	190616	PF3D7_0104300	UBP1	c.348A>G	1.0
Pf3D7_01_v3	190739	PF3D7_0104300	UBP1	p.Asn157Lys	1.0
Pf3D7_01_v3	190967	PF3D7_0104300	UBP1	c.699_700insAATAGTATTAATAATAGTATTAAT	0.57
Pf3D7_01_v3	191432	PF3D7_0104300	UBP1	c.1162_1164dupGAT	0.83
Pf3D7_01_v3	192111	PF3D7_0104300	UBP1	p.Tyr615His	1.0
Pf3D7_01_v3	193667	PF3D7_0104300	UBP1	p.Arg1133Ser	0.95
Pf3D7_01_v3	194117	PF3D7_0104300	UBP1	c.3849T>C	1.0
Pf3D7_01_v3	196010	PF3D7_0104300	UBP1	p.Lys1914Asn	1.0
Pf3D7_01_v3	196011	PF3D7_0104300	UBP1	p.Glu1915Lys	1.0
Pf3D7_01_v3	196981	PF3D7_0104300	UBP1	p.Arg2238Lys	0.98
Pf3D7_01_v3	199865	PF3D7_0104300	UBP1	c.9365_9391delGTATGAATCATGCAAACCGTGTGAGTC	0.53
Pf3D7_01_v3	380532	PF3D7_0109800	PF3D7_0109800	c.-165A>G	1.0
Pf3D7_01_v3	381402	PF3D7_0109800	PF3D7_0109800	c.704_706dupATA	0.94
Pf3D7_03_v3	922867	PF3D7_0321900	CARL	c.-106_-105delAT	0.95
Pf3D7_03_v3	925808	PF3D7_0321900	CARL	p.Lys903Glu	1.0
Pf3D7_04_v3	748516	PF3D7_0417200	DHFR-TS	c.429T>C	0.98
Pf3D7_05_v3	410338	PF3D7_0509800	PI4K	p.His24Leu	1.0
Pf3D7_05_v3	412895	PF3D7_0509800	PI4K	c.2628C>T	0.76
Pf3D7_05_v3	412896	PF3D7_0509800	PI4K	p.Asn877Asp	0.76
Pf3D7_05_v3	413426	PF3D7_0509800	PI4K	c.3159C>T	0.97
Pf3D7_05_v3	413958	PF3D7_0509800	PI4K	c.3689_3691dupATA	1.0
Pf3D7_05_v3	415296	PF3D7_0509800	PI4K	c.4668T>C	1.0
Pf3D7_05_v3	959837	PF3D7_0523000	MDR1	p.Asp650Asn	0.94
Pf3D7_05_v3	959843	PF3D7_0523000	MDR1	p.Asn652Asp	0.94
Pf3D7_05_v3	960046	PF3D7_0523000	MDR1	c.2157C>T	1.0
Pf3D7_07_v3	894384	PF3D7_0720700	PF3D7_0720700	c.2175C>G	1.0
Pf3D7_07_v3	895180	PF3D7_0720700	PF3D7_0720700	p.Asn991Asp	1.0
Pf3D7_07_v3	896099	PF3D7_0720700	PF3D7_0720700	c.3890_3891insAAACAATGT	0.78
Pf3D7_07_v3	897236	PF3D7_0720700	PF3D7_0720700	c.5028_5036delTGTAAAAAG	1.0
Pf3D7_07_v3	898242	PF3D7_0720700	PF3D7_0720700	c.6033C>A	1.0
Pf3D7_08_v3	548068	PF3D7_0810800	PPPK-DHPS	c.-131_-130delAT	1.0
Pf3D7_08_v3	548801	PF3D7_0810800	PPPK-DHPS	c.426G>A	1.0
Pf3D7_08_v3	643648	PF3D7_0813000	PF3D7_0813000	c.1229_1237dupATAATATGA	0.74
Pf3D7_08_v3	644383	PF3D7_0813000	PF3D7_0813000	c.491_502delGAGATAAAGATA	1.0
Pf3D7_10_v3	1046204	PF3D7_1025000	PF3D7_1025000	p.Arg859Lys	1.0
Pf3D7_10_v3	1046830	PF3D7_1025000	PF3D7_1025000	c.1950A>T	0.95
Pf3D7_10_v3	1047084	PF3D7_1025000	PF3D7_1025000	p.Asn566Asp	1.0
Pf3D7_10_v3	1047087	PF3D7_1025000	PF3D7_1025000	p.Asn565Asp	1.0
Pf3D7_10_v3	1047093	PF3D7_1025000	PF3D7_1025000	p.Tyr563Asp	1.0
Pf3D7_10_v3	1047095	PF3D7_1025000	PF3D7_1025000	p.Thr562Glu	1.0
Pf3D7_10_v3	1047108	PF3D7_1025000	PF3D7_1025000	p.Asn558Asp	1.0
Pf3D7_10_v3	1047111	PF3D7_1025000	PF3D7_1025000	p.AsnAsn556LysTyr	1.0
Pf3D7_10_v3	1047113	PF3D7_1025000	PF3D7_1025000	p.Asn556Thr	1.0
Pf3D7_10_v3	1047117	PF3D7_1025000	PF3D7_1025000	p.Asp555Asn	1.0
Pf3D7_10_v3	1047120	PF3D7_1025000	PF3D7_1025000	p.Tyr554Asn	1.0
Pf3D7_10_v3	1047122	PF3D7_1025000	PF3D7_1025000	p.Thr553Lys	1.0
Pf3D7_10_v3	1047135	PF3D7_1025000	PF3D7_1025000	p.Asn549Asp	1.0
Pf3D7_10_v3	1047138	PF3D7_1025000	PF3D7_1025000	p.AsnAsn547LysTyr	1.0
Pf3D7_10_v3	1047140	PF3D7_1025000	PF3D7_1025000	p.Asn547Thr	1.0
Pf3D7_10_v3	1047143	PF3D7_1025000	PF3D7_1025000	c.1631_1636delCATATG	1.0
Pf3D7_10_v3	1047323	PF3D7_1025000	PF3D7_1025000	p.Phe486Ser	0.98
Pf3D7_10_v3	1047779	PF3D7_1025000	PF3D7_1025000	p.Gly334Glu	1.0
Pf3D7_10_v3	1449646	PF3D7_1036800	PF3D7_1036800	p.Thr459Ile	1.0
Pf3D7_10_v3	1451029	PF3D7_1036800	PF3D7_1036800	p.Arg104Lys	1.0
Pf3D7_11_v3	1526106	PF3D7_1138700	PF3D7_1138700	p.Ser1721Ala	1.0
Pf3D7_11_v3	1528120	PF3D7_1138700	PF3D7_1138700	p.Glu1049Asp	0.96
Pf3D7_11_v3	1529369	PF3D7_1138700	PF3D7_1138700	p.Ser633Asn	1.0
Pf3D7_11_v3	1529778	PF3D7_1138700	PF3D7_1138700	p.Glu497Gln	1.0
Pf3D7_11_v3	1529908	PF3D7_1138700	PF3D7_1138700	c.1359T>C	1.0
Pf3D7_12_v3	529418	PF3D7_1211900	ATP4	p.Gly1128Arg	1.0
Pf3D7_12_v3	529559	PF3D7_1211900	ATP4	p.Gln1081Lys	1.0
Pf3D7_12_v3	532887	PF3D7_1211900	ATP4	c.-88A>C	0.98
Pf3D7_12_v3	532889	PF3D7_1211900	ATP4	c.-90C>A	0.98
Pf3D7_12_v3	592234	PF3D7_1213800	PRS	c.201G>A	1.0
Pf3D7_12_v3	592496	PF3D7_1213800	PRS	c.-62G>A	1.0
Pf3D7_12_v3	592610	PF3D7_1213800	PRS	c.-196_-177delAATATATATATATATATATA	0.95
Pf3D7_12_v3	1927229	PF3D7_1246300	PF3D7_1246300	c.1041T>C	1.0
Pf3D7_12_v3	2092045	PF3D7_1251200	PF3D7_1251200	c.-42_-41insATATAT	1.0
Pf3D7_12_v3	2092969	PF3D7_1251200	PF3D7_1251200	p.Ser183Gly	1.0
Pf3D7_12_v3	2093058	PF3D7_1251200	PF3D7_1251200	c.636A>G	1.0
Pf3D7_13_v3	1726432	PF3D7_1343700	K13	p.Lys189Thr	1.0
Pf3D7_13_v3	1727052	PF3D7_1343700	K13	c.-55A>T	0.93
Pf3D7_13_v3	1727056	PF3D7_1343700	K13	c.-59A>T	0.93
Pf3D7_13_v3	1727071	PF3D7_1343700	K13	c.-104_-75delAATATATATATATATATATATATATATATA	0.93
Pf3D7_14_v3	1550691	PF3D7_1438400	MCA2	p.Asp226Glu	1.0
Pf3D7_14_v3	1550916	PF3D7_1438400	MCA2	c.904_906delAAT	1.0
Pf3D7_14_v3	1553197	PF3D7_1438400	MCA2	p.Glu1062Gln	1.0
Pf3D7_14_v3	1553266	PF3D7_1438400	MCA2	p.Asn1085Asp	1.0
Pf3D7_14_v3	1553649	PF3D7_1438400	MCA2	c.3636C>T	1.0
Pf3D7_14_v3	1553661	PF3D7_1438400	MCA2	c.3648T>C	1.0
Pf3D7_14_v3	1553697	PF3D7_1438400	MCA2	c.3684C>T	1.0
Pf3D7_14_v3	1554029	PF3D7_1438400	MCA2	p.Glu1339Ala	1.0
Pf3D7_14_v3	1554098	PF3D7_1438400	MCA2	p.Thr1362Ile	1.0
Pf3D7_14_v3	1554318	PF3D7_1438400	MCA2	c.4305G>A	1.0
Pf3D7_14_v3	2090784	PF3D7_1451100	eEF2	c.-118_-117insAT	0.75
Pf3D7_14_v3	2480289	PF3D7_1460900	ARPS10	c.-151T>A	1.0

QC failed variants

Chromosome:	Genome Position	Locus Tag	Gene Name	Change	Estimated fraction
Pf3D7_01_v3	191090	PF3D7_0104300	UBP1	p.Asn274Lys	0.23
Pf3D7_01_v3	192530	PF3D7_0104300	UBP1	p.Asn754Lys	1.0
Pf3D7_01_v3	192533	PF3D7_0104300	UBP1	c.2265A>G	1.0
Pf3D7_01_v3	192633	PF3D7_0104300	UBP1	p.Asn789Asp	1.0
Pf3D7_01_v3	192640	PF3D7_0104300	UBP1	c.2373_2405delCGATGATGATGACGATGACAATGATGATGATGA	1.0
Pf3D7_04_v3	747914	PF3D7_0417200	DHFR-TS	c.-174C>A	0.17
Pf3D7_04_v3	747993	PF3D7_0417200	DHFR-TS	c.-95C>A	0.19
Pf3D7_04_v3	747997	PF3D7_0417200	DHFR-TS	c.-91C>A	0.15
Pf3D7_05_v3	410075	PF3D7_0509800	PI4K	c.-193C>A	0.15
Pf3D7_05_v3	410184	PF3D7_0509800	PI4K	c.-84C>A	0.16
Pf3D7_05_v3	410271	PF3D7_0509800	PI4K	p.Glu2*	0.1
Pf3D7_05_v3	410566	PF3D7_0509800	PI4K	p.Val100Ala	1.0
Pf3D7_05_v3	410608	PF3D7_0509800	PI4K	p.Gly114Asp	1.0
Pf3D7_05_v3	410611	PF3D7_0509800	PI4K	p.Asp115Gly	1.0
Pf3D7_05_v3	410638	PF3D7_0509800	PI4K	p.Gly124Asp	1.0
Pf3D7_05_v3	410644	PF3D7_0509800	PI4K	p.Asp126Gly	1.0
Pf3D7_05_v3	410656	PF3D7_0509800	PI4K	p.Asp130Gly	1.0
Pf3D7_05_v3	410668	PF3D7_0509800	PI4K	p.Asp134Gly	1.0
Pf3D7_05_v3	412890	PF3D7_0509800	PI4K	p.Asp875Asn	0.64
Pf3D7_07_v3	403519	PF3D7_0709000	CRT	p.Leu41Ile	0.2
Pf3D7_07_v3	403532	PF3D7_0709000	CRT	p.Ala45Asp	0.17
Pf3D7_07_v3	403546	PF3D7_0709000	CRT	p.Leu50Ile	0.13
Pf3D7_07_v3	403621	PF3D7_0709000	CRT	p.Asn75Glu	1.0
Pf3D7_07_v3	404032	PF3D7_0709000	CRT	p.Thr152Asn	0.29
Pf3D7_07_v3	404570	PF3D7_0709000	CRT	c.668C>A	0.17
Pf3D7_07_v3	405838	PF3D7_0709000	CRT	p.Arg371Ile	1.0
Pf3D7_07_v3	892492	PF3D7_0720700	PF3D7_0720700	c.285-2A>G	0.67
Pf3D7_07_v3	892493	PF3D7_0720700	PF3D7_0720700	c.285-1G>A	0.67
Pf3D7_07_v3	892495	PF3D7_0720700	PF3D7_0720700	c.286C>T	0.67
Pf3D7_07_v3	895153	PF3D7_0720700	PF3D7_0720700	p.Asp982Asn	0.2
Pf3D7_07_v3	896100	PF3D7_0720700	PF3D7_0720700	c.3891G>A	0.1
Pf3D7_08_v3	644936	PF3D7_0813000	PF3D7_0813000	c.-51C>A	1.0
Pf3D7_08_v3	645031	PF3D7_0813000	PF3D7_0813000	c.-147_-146insT	1.0
Pf3D7_10_v3	1049857	PF3D7_1025000	PF3D7_1025000	c.-97G>A	0.22
Pf3D7_10_v3	1049903	PF3D7_1025000	PF3D7_1025000	c.-145_-144delAT	1.0
Pf3D7_10_v3	1451758	PF3D7_1036800	PF3D7_1036800	c.-112G>T	0.14
Pf3D7_10_v3	1451781	PF3D7_1036800	PF3D7_1036800	c.-135C>A	0.29
Pf3D7_10_v3	1451794	PF3D7_1036800	PF3D7_1036800	c.-148C>T	0.8
Pf3D7_12_v3	209707	PF3D7_1204400	PF3D7_1204400	p.Cys166Phe	0.2
Pf3D7_12_v3	1925464	PF3D7_1246300	PF3D7_1246300	c.-178C>A	0.11
Pf3D7_12_v3	1925484	PF3D7_1246300	PF3D7_1246300	c.-158G>A	1.0
Pf3D7_12_v3	1925560	PF3D7_1246300	PF3D7_1246300	c.-81_-78delTATA	0.29
Pf3D7_12_v3	2091948	PF3D7_1251200	PF3D7_1251200	c.-139C>T	0.16
Pf3D7_12_v3	2091959	PF3D7_1251200	PF3D7_1251200	c.-128C>T	0.22
Pf3D7_12_v3	2092303	PF3D7_1251200	PF3D7_1251200	p.Cys25*	0.12
Pf3D7_12_v3	2092314	PF3D7_1251200	PF3D7_1251200	p.Thr29Asn	0.19
Pf3D7_12_v3	2092341	PF3D7_1251200	PF3D7_1251200	p.Ala38Asp	0.14
Pf3D7_12_v3	2092353	PF3D7_1251200	PF3D7_1251200	c.125C>A	0.12
Pf3D7_13_v3	749141	PF3D7_1318100	PF3D7_1318100	c.-170A>G	0.11
Pf3D7_13_v3	846960	PF3D7_1320600	RAB11a	c.-130G>T	0.14
Pf3D7_13_v3	847089	PF3D7_1320600	RAB11a	c.-1G>T	0.22
Pf3D7_13_v3	847120	PF3D7_1320600	RAB11a	p.Leu11Met	0.22
Pf3D7_13_v3	847305	PF3D7_1320600	RAB11a	c.43G>T	0.13
Pf3D7_14_v3	1548768	PF3D7_1438400	MCA2	c.-150C>T	0.25
Pf3D7_14_v3	1548803	PF3D7_1438400	MCA2	c.-115C>A	0.31
Pf3D7_14_v3	1550410	PF3D7_1438400	MCA2	p.Met133Val	0.31
Pf3D7_14_v3	1550437	PF3D7_1438400	MCA2	p.Met142Val	0.31
Pf3D7_14_v3	1550446	PF3D7_1438400	MCA2	p.Val145Met	0.31
Pf3D7_14_v3	1550472	PF3D7_1438400	MCA2	c.451_459dupGTGAATAAT	0.29
Pf3D7_14_v3	1550473	PF3D7_1438400	MCA2	p.Met154Val	0.13
Pf3D7_14_v3	1550491	PF3D7_1438400	MCA2	p.Val160Met	0.13
Pf3D7_14_v3	1550500	PF3D7_1438400	MCA2	p.Met163Val	0.13
Pf3D7_14_v3	1551744	PF3D7_1438400	MCA2	c.1731A>T	0.22
Pf3D7_14_v3	1551755	PF3D7_1438400	MCA2	c.1743_1745delAAA	0.22
Pf3D7_14_v3	1553546	PF3D7_1438400	MCA2	p.Ala1178Asp	0.11
Pf3D7_14_v3	1554043	PF3D7_1438400	MCA2	p.Tyr1344Lys	1.0
Pf3D7_14_v3	1556509	PF3D7_1438400	MCA2	p.Gly1997Glu	0.43

RESISTANCE REPORT OTHER VARIANTS QC FAIL VARIANTS MISSING POSITIONS REPORT

Resistance variants report

Gene	Mutations
MDR1	p.Asn86Tyr p.Tyr184Phe VIEW IN IGV
CRT	p.Met74Ile p.Lys76Thr p.Ala220Ser p.Gln271Glu VIEW IN IGV
PPPK-DHPS	p.Ala437Gly VIEW IN IGV

Other variants

Gene	Mutations
UBP1	c.348A>G p.Asn157Lys c.699_700insAATAGTATTAATAATAGTATTAAT c.1162_1164dupGAT p.Tyr615His p.Arg1133Ser c.3849T>C p.Lys1914Asn p.Glu1915Lys p.Arg2238Lys c.9365_9391delGTATGAATCATGCAAACCGTGTGAGTC VIEW IN IGV
PF3D7_0109800	c.-165A>G c.704_706dupATA VIEW IN IGV
CARL	c.-106_-105delAT p.Lys903Glu VIEW IN IGV
DHFR-TS	c.429T>C VIEW IN IGV
PI4K	p.His24Leu c.2628C>T p.Asn877Asp c.3159C>T c.3689_3691dupATA c.4668T>C VIEW IN IGV
MDR1	p.Asp650Asn p.Asn652Asp c.2157C>T VIEW IN IGV
PF3D7_0720700	c.2175C>G p.Asn991Asp c.3890_3891insAAACAATGT c.5028_5036delTGTAAAAAG c.6033C>A VIEW IN IGV
PPPK-DHPS	c.-131_-130delAT c.426G>A VIEW IN IGV
PF3D7_0813000	c.1229_1237dupATAATATGA c.491_502delGAGATAAAGATA VIEW IN IGV
PF3D7_1025000	p.Arg859Lys c.1950A>T p.Asn566Asp p.Asn565Asp p.Tyr563Asp p.Thr562Glu p.Asn558Asp p.AsnAsn556LysTyr p.Asn556Thr p.Asp555Asn p.Tyr554Asn p.Thr553Lys p.Asn549Asp p.AsnAsn547LysTyr p.Asn547Thr c.1631_1636delCATATG p.Phe486Ser p.Gly334Glu VIEW IN IGV
PF3D7_1036800	p.Thr459Ile p.Arg104Lys VIEW IN IGV
PF3D7_1138700	p.Ser1721Ala p.Glu1049Asp p.Ser633Asn p.Glu497Gln c.1359T>C VIEW IN IGV
ATP4	p.Gly1128Arg p.Gln1081Lys c.-88A>C c.-90C>A VIEW IN IGV
PRS	c.201G>A c.-62G>A c.-196_-177delAATATATATATATATATATA VIEW IN IGV
PF3D7_1246300	c.1041T>C VIEW IN IGV
PF3D7_1251200	c.-42_-41insATATAT p.Ser183Gly c.636A>G VIEW IN IGV
K13	p.Lys189Thr c.-55A>T c.-59A>T c.-104_-75delAATATATATATATATATATATATATATATA VIEW IN IGV
MCA2	p.Asp226Glu c.904_906delAAT p.Glu1062Gln p.Asn1085Asp c.3636C>T c.3648T>C c.3684C>T p.Glu1339Ala p.Thr1362Ile c.4305G>A VIEW IN IGV
eEF2	c.-118_-117insAT VIEW IN IGV
ARPS10	c.-151T>A VIEW IN IGV

QC failed variants

Gene	Mutations
UBP1	VIEW IN IGV
DHFR-TS	VIEW IN IGV
PI4K	VIEW IN IGV
CRT	VIEW IN IGV
PF3D7_0720700	VIEW IN IGV
PF3D7_0813000	VIEW IN IGV
PF3D7_1025000	VIEW IN IGV
PF3D7_1036800	VIEW IN IGV
PF3D7_1204400	VIEW IN IGV
PF3D7_1246300	VIEW IN IGV
PF3D7_1251200	VIEW IN IGV
PF3D7_1318100	VIEW IN IGV
RAB11a	VIEW IN IGV
MCA2	VIEW IN IGV

Missing positions report

Gene	Mutations

BACK

Estimated Region of Origin

Western Africa - 100.0%

BACK

Analysis

Process	Software
Software	{'taxonomic_software': 'sourmash', 'trimming': 'trimmomatic', 'mapping': 'bwa', 'variant_calling': 'freebayes-Haplotype', 'depth_calculation': 'samtools'}

BACK

Coverage report

Gene	Percentage depth passed	Median Depth
UBP1	99.92	40.0
PF3D7_0109800	100.0	38.0
CARL	100.0	33.0
DHFR-TS	100.0	43.0
PI4K	100.0	39.0
MDR1	100.0	39.0
DHODH	100.0	43.0
CRT	99.48	24.0
PF3D7_0720700	100.0	40.0
PPPK-DHPS	100.0	39.0
PF3D7_0813000	100.0	38.0
PF3D7_1025000	99.91	43.0
PF3D7_1036800	100.0	35.0
PF3D7_1113300	100.0	32.0
PF3D7_1138700	100.0	42.0
PF3D7_1204400	100.0	27.0
ATP4	100.0	45.0
PRS	100.0	40.0
AP2-MU	100.0	34.0
PF3D7_1246300	100.0	31.0
PF3D7_1251200	100.0	36.0
PF3D7_1318100	100.0	33.0
RAB11a	100.0	26.0
K13	100.0	42.0
MCA2	100.0	37.0
eEF2	100.0	43.0
ARPS10	100.0	29.0
CYTB	100.0	960.0

BACK

Species

Species	ANI	Abundance	Accession
Plasmodium falciparum	99.8 %	35.68	Plasmodium_falciparum

BACK

Welcome to the results screen

RESULT ID: 90f2cb47-60c6-41c0-a50b-a06b70dcd5f6

FASTQ FILE NAME: ERR1008804_1.fastq.gz

Species view

Species

Genomic variants

Genomic variants

Sample location

Estimated Region of Origin

Est Moi

Analysis

Coverage Report

Coverage report

IGV

IGV section

RESULT ID

SPECIES

GENOMIC VARIANTS

ESTIMATED ORIGIN OF REGION

ANALYSIS

COVERAGE REPORT

SHOW MORE INFO

RESULT ID: 90f2cb47-60c6-41c0-a50b-a06b70dcd5f6

Species

Genomic variants

Estimated Region of Origin

Analysis

Coverage report

Species