TB-Profiler result

Run: SRR3732595
Summary

Run ID: SRR3732595

Sample name:

Date: 04-04-2023 05:36:30

Number of reads: 550459

Percentage reads mapped: 99.49

Strain: lineage4

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155341 p.Met257Ile missense_variant 0.2 isoniazid
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5710 c.471C>A synonymous_variant 0.33
gyrB 6719 p.Asp494Tyr missense_variant 0.5
gyrB 7154 p.Asp639Tyr missense_variant 0.67
gyrA 7520 c.219G>T synonymous_variant 0.18
gyrA 7544 p.Met81Ile missense_variant 0.5
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490732 c.-51C>A upstream_gene_variant 0.67
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491772 c.990C>A synonymous_variant 1.0
mshA 575255 c.-93G>T upstream_gene_variant 1.0
mshA 575591 c.244C>A synonymous_variant 0.22
mshA 575626 c.279C>A synonymous_variant 0.18
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575969 p.Asp208Tyr missense_variant 0.29
mshA 576032 p.Gly229Cys missense_variant 0.33
mshA 576373 c.1026G>T synonymous_variant 0.17
mshA 576459 p.Ala371Gly missense_variant 0.33
rpoB 760350 p.Asp182Tyr missense_variant 0.67
rpoB 760460 c.654G>T synonymous_variant 0.33
rpoB 761246 c.1440C>A synonymous_variant 0.5
rpoB 761428 p.Pro541Leu missense_variant 0.18
rpoB 761782 p.Gly659Val missense_variant 0.67
rpoB 762221 p.Glu805Asp missense_variant 0.4
rpoB 763290 p.Arg1162Ser missense_variant 1.0
rpoC 764041 p.Ser224Arg missense_variant 1.0
rpoC 765295 c.1926G>T synonymous_variant 0.22
rpoC 765378 p.Arg670Leu missense_variant 0.25
rpoC 765848 p.Pro827Thr missense_variant 1.0
rpoC 765904 c.2535C>A synonymous_variant 0.5
rpoC 766736 p.Arg1123Trp missense_variant 0.33
rpoC 766749 p.Pro1127His missense_variant 0.29
rpoC 766784 p.Gln1139Lys missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776103 p.Ile793Thr missense_variant 0.5
mmpL5 776499 p.Gly661Val missense_variant 0.4
mmpL5 777342 p.Arg380His missense_variant 0.22
mmpL5 777355 p.Val376Leu missense_variant 0.17
mmpL5 777368 p.Lys371Asn missense_variant 0.17
mmpS5 778792 p.Leu38Phe missense_variant 0.4
mmpL5 779187 c.-707C>T upstream_gene_variant 0.67
mmpS5 779620 c.-715G>T upstream_gene_variant 0.67
rplC 800624 c.-185G>T upstream_gene_variant 0.5
fbiC 1303197 p.Lys89Asn missense_variant 0.22
fbiC 1303217 p.Arg96Leu missense_variant 0.25
fbiC 1304133 c.1203G>T synonymous_variant 0.17
fbiC 1304355 c.1425G>T synonymous_variant 0.33
fbiC 1304362 p.Glu478* stop_gained 0.5
fbiC 1304649 p.Asp573Glu missense_variant 0.4
Rv1258c 1406755 p.Ala196Thr missense_variant 0.5
Rv1258c 1406767 p.Gln192Lys missense_variant 0.4
Rv1258c 1407157 p.Ala62Ser missense_variant 0.2
embR 1416468 p.Asp294Tyr missense_variant 0.5
embR 1417219 c.129C>A synonymous_variant 0.5
atpE 1461156 p.Gly38Cys missense_variant 0.67
rrs 1471718 n.-128G>T upstream_gene_variant 1.0
fabG1 1673941 p.Ala168Thr missense_variant 0.25
fabG1 1673947 p.Glu170* stop_gained 0.25
inhA 1674510 p.Met103Ile missense_variant 0.5
rpsA 1834406 p.Arg289Ser missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918596 c.657C>A synonymous_variant 0.33
ndh 2101697 p.Ala449Val missense_variant 0.5
ndh 2102157 p.Glu296* stop_gained 1.0
ndh 2102188 p.Leu285Phe missense_variant 0.67
ndh 2102232 p.Ser271Pro missense_variant 0.5
ndh 2102254 p.Asp263Glu missense_variant 1.0
ndh 2102686 c.357G>T synonymous_variant 1.0
ndh 2102970 p.Gly25Cys missense_variant 0.67
ndh 2103123 c.-81G>A upstream_gene_variant 0.5
katG 2153982 c.2130C>T synonymous_variant 0.29
katG 2155354 p.Arg253Leu missense_variant 0.22
katG 2155419 p.Asn231Lys missense_variant 0.25
katG 2155448 p.Ala222Thr missense_variant 0.67
PPE35 2167740 p.Thr958Ile missense_variant 0.33
PPE35 2170107 p.Ala169Val missense_variant 0.2
PPE35 2170293 p.Pro107Leu missense_variant 0.67
Rv1979c 2222501 p.Ala222Thr missense_variant 1.0
Rv1979c 2222548 p.Ser206* stop_gained 0.5
Rv1979c 2223130 p.His12Arg missense_variant 0.5
Rv1979c 2223152 p.Arg5Trp missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288737 p.Val169Ile missense_variant 0.33
pncA 2288738 c.504C>A synonymous_variant 0.33
pncA 2288760 p.Ala161Glu missense_variant 0.4
pncA 2289415 c.-174C>A upstream_gene_variant 0.67
pncA 2289705 c.-464G>T upstream_gene_variant 0.29
pncA 2289733 c.-492G>T upstream_gene_variant 0.33
pncA 2289828 c.-587C>A upstream_gene_variant 0.5
pncA 2289839 c.-598G>A upstream_gene_variant 0.4
pncA 2290112 c.-871C>T upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518456 c.342C>A synonymous_variant 0.4
kasA 2518738 c.624G>T synonymous_variant 0.33
kasA 2518755 p.Arg214Leu missense_variant 0.33
kasA 2519058 p.Thr315Met missense_variant 0.18
eis 2714902 p.Arg144Gln missense_variant 0.67
eis 2715054 c.279G>A synonymous_variant 0.25
eis 2715077 p.Ala86Thr missense_variant 0.29
ahpC 2726172 c.-21G>A upstream_gene_variant 0.5
folC 2747055 p.Asp182Tyr missense_variant 1.0
folC 2747696 c.-98G>A upstream_gene_variant 0.22
pepQ 2859321 c.1098C>A synonymous_variant 0.5
pepQ 2859666 p.Gln251His missense_variant 0.5
pepQ 2859789 c.630G>T synonymous_variant 0.25
pepQ 2859899 p.Arg174Cys missense_variant 0.29
pepQ 2860518 c.-100C>A upstream_gene_variant 0.33
ribD 2986721 c.-118G>A upstream_gene_variant 0.25
ribD 2986733 c.-106C>A upstream_gene_variant 0.25
ribD 2987064 p.Glu76* stop_gained 0.33
Rv2752c 3064589 p.Arg535Ser missense_variant 0.4
Rv2752c 3065172 c.1020G>T synonymous_variant 0.4
Rv2752c 3065438 p.Ala252Thr missense_variant 1.0
thyX 3067237 p.Asp237Asn missense_variant 0.22
ald 3086878 p.Pro20Leu missense_variant 1.0
fbiD 3339150 c.33C>A synonymous_variant 0.25
fbiD 3339198 c.81C>A synonymous_variant 0.29
fbiD 3339500 p.Ala128Glu missense_variant 0.15
fbiD 3339720 c.603C>A synonymous_variant 0.29
Rv3083 3448315 c.-189C>A upstream_gene_variant 0.18
Rv3083 3448703 p.Arg67His missense_variant 1.0
Rv3083 3448730 p.Ala76Asp missense_variant 0.67
Rv3083 3448909 p.Leu136Ile missense_variant 0.67
Rv3083 3449943 c.1440C>T synonymous_variant 0.67
fprA 3475351 p.Glu449* stop_gained 0.2
Rv3236c 3612061 c.1056C>A synonymous_variant 0.67
fbiA 3641215 p.Ala225Ser missense_variant 0.4
fbiA 3641371 p.Gly277Cys missense_variant 0.33
fbiA 3641456 p.Ser305* stop_gained 0.4
fbiB 3641730 p.Asp66Tyr missense_variant 0.5
fbiB 3642317 p.Arg261Ser missense_variant 0.17
fbiB 3642611 p.Ser359Arg missense_variant 0.25
alr 3840923 c.498C>A synonymous_variant 0.5
clpC1 4039682 c.1023C>A synonymous_variant 0.67
embC 4239859 c.-4C>A upstream_gene_variant 0.5
embC 4240340 p.His160Asn missense_variant 0.29
embC 4240360 c.498C>A synonymous_variant 0.4
embC 4240894 p.Met344Ile missense_variant 0.67
embC 4241642 p.Ala594Thr missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243015 c.-218C>T upstream_gene_variant 0.67
embC 4243070 p.Ala1070Thr missense_variant 0.33
embA 4244044 p.Ser271* stop_gained 0.5
embA 4244169 p.Gln313Lys missense_variant 0.4
embA 4244215 p.Ala328Asp missense_variant 0.4
embA 4245079 p.Trp616* stop_gained 0.33
embB 4247060 p.Pro183Thr missense_variant 0.4
embB 4247108 p.Gly199Trp missense_variant 0.33
embB 4247886 p.Gly458Val missense_variant 0.29
embB 4248590 p.Ala693Ser missense_variant 0.29
embB 4248981 p.Ser823Ile missense_variant 1.0
embB 4249184 p.Gly891Trp missense_variant 0.5
embB 4249334 p.Ala941Thr missense_variant 0.25
aftB 4267557 p.Ala427Val missense_variant 0.5
aftB 4267873 p.Gln322Glu missense_variant 1.0
ethA 4326740 p.Arg245Leu missense_variant 0.67
ethA 4326879 p.Ala199Thr missense_variant 0.4
ethA 4328214 c.-741C>A upstream_gene_variant 0.33
whiB6 4338409 p.Pro38His missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407743 p.Arg154Trp missense_variant 0.29