TB-Profiler result

Run: SRR2101360
Summary

Run ID: SRR2101360

Sample name:

Date: 03-04-2023 23:40:25

Number of reads: 588774

Percentage reads mapped: 95.67

Strain: lineage4.1.2.1

Drug-resistance: MDR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289031 p.His71Tyr missense_variant 1.0 pyrazinamide
ald 3086951 c.133delA frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol
gid 4407802 p.Ala134Glu missense_variant 1.0 streptomycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491043 c.261T>G synonymous_variant 0.14
fgd1 491049 c.267T>G synonymous_variant 0.14
fgd1 491063 p.Gly94Ala missense_variant 0.15
fgd1 491077 p.Asn99Asp missense_variant 0.12
fgd1 491082 c.300T>G synonymous_variant 0.12
fgd1 491085 c.303T>G synonymous_variant 0.12
fgd1 491286 c.504G>C synonymous_variant 0.12
fgd1 491292 c.510G>C synonymous_variant 0.13
fgd1 491296 p.Val172Ile missense_variant 0.13
fgd1 491302 p.Ile174Val missense_variant 0.13
fgd1 491322 c.540G>C synonymous_variant 0.14
fgd1 491325 c.543G>C synonymous_variant 0.13
fgd1 491328 c.546C>G synonymous_variant 0.13
fgd1 491331 c.549G>A synonymous_variant 0.12
fgd1 491340 c.558C>A synonymous_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576537 p.Gln397Leu missense_variant 0.13
ccsA 620198 p.Gln103Leu missense_variant 0.18
ccsA 620208 c.318G>C synonymous_variant 0.17
ccsA 620226 c.336G>A synonymous_variant 0.17
ccsA 620245 c.355T>C synonymous_variant 0.15
ccsA 620249 p.Ser120Cys missense_variant 0.18
ccsA 620256 c.366C>G synonymous_variant 0.18
ccsA 620265 c.375C>G synonymous_variant 0.18
ccsA 620283 c.393T>G synonymous_variant 0.12
ccsA 620284 p.Ala132Pro missense_variant 0.12
ccsA 620288 p.Arg133Gln missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 0.97
rpoB 761354 c.1548C>G synonymous_variant 0.25
rpoB 761360 c.1554T>C synonymous_variant 0.22
rpoB 761362 p.Ser519Thr missense_variant 0.22
rpoB 761375 c.1569G>C synonymous_variant 0.22
rpoB 761408 c.1602G>T synonymous_variant 0.18
rpoB 761414 c.1608A>G synonymous_variant 0.17
rpoB 761423 c.1617T>C synonymous_variant 0.2
rpoB 761435 c.1629T>C synonymous_variant 0.2
rpoB 761437 p.Ala544Asp missense_variant 0.2
rpoB 761439 p.Asp545Asn missense_variant 0.2
rpoB 761444 c.1638T>C synonymous_variant 0.2
rpoB 761471 c.1665C>G synonymous_variant 0.13
rpoC 762749 c.-621C>G upstream_gene_variant 0.12
rpoC 762753 c.-617T>C upstream_gene_variant 0.13
rpoB 762759 p.Cys985Ala missense_variant 0.12
rpoC 762782 c.-588T>C upstream_gene_variant 0.13
rpoB 762785 p.Asp993Glu missense_variant 0.13
rpoC 762788 c.-582G>C upstream_gene_variant 0.13
rpoB 762789 p.Leu995Met missense_variant 0.13
rpoB 762799 p.Ala998Gly missense_variant 0.12
rpoC 762812 c.-558C>G upstream_gene_variant 0.12
rpoB 762813 p.Met1003Val missense_variant 0.12
rpoC 762836 c.-534C>T upstream_gene_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776238 p.Gly748Asp missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406813 c.528T>C synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.13
inhA 1673646 c.-556T>C upstream_gene_variant 0.18
inhA 1673652 c.-550C>G upstream_gene_variant 0.18
fabG1 1673657 p.Thr73Lys missense_variant 0.15
inhA 1673660 c.-542C>A upstream_gene_variant 0.15
inhA 1673664 c.-538A>C upstream_gene_variant 0.15
inhA 1673667 c.-535A>G upstream_gene_variant 0.15
fabG1 1673758 p.Lys107Glu missense_variant 0.12
inhA 1673772 c.-430C>G upstream_gene_variant 0.12
fabG1 1673864 p.Ser142Tyr missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102679 p.Gly122Cys missense_variant 0.15
katG 2155614 p.Val166Ile missense_variant 0.14
katG 2155617 c.495T>C synonymous_variant 0.14
katG 2155626 c.486G>C synonymous_variant 0.13
katG 2155641 p.Lys157Asn missense_variant 0.13
katG 2155680 c.432G>C synonymous_variant 0.13
katG 2155691 c.421T>C synonymous_variant 0.15
katG 2155696 p.Ala139Val missense_variant 0.15
katG 2155716 c.396T>G synonymous_variant 0.15
katG 2155722 c.390G>C synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726264 c.72C>G synonymous_variant 0.12
ahpC 2726288 c.96C>T synonymous_variant 0.17
pepQ 2860530 c.-112T>C upstream_gene_variant 0.14
ribD 2987245 p.Thr136Asn missense_variant 0.25
thyX 3067249 p.Thr233Ser missense_variant 0.13
thyX 3067250 p.Val232Ile missense_variant 0.13
thyX 3067654 p.His98Tyr missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641540 c.8delG frameshift_variant 0.12
fbiB 3641921 c.387C>T synonymous_variant 0.17
fbiB 3642331 p.Phe266Ser missense_variant 0.25
alr 3840259 p.Tyr388Asp missense_variant 1.0
rpoA 3877986 c.522G>C synonymous_variant 0.14
rpoA 3877989 c.519A>G synonymous_variant 0.14
rpoA 3878001 c.507A>G synonymous_variant 0.14
rpoA 3878022 c.486T>C synonymous_variant 0.18
rpoA 3878028 c.480G>T synonymous_variant 0.17
rpoA 3878031 c.477T>C synonymous_variant 0.17
rpoA 3878040 c.468T>C synonymous_variant 0.15
rpoA 3878043 c.465G>C synonymous_variant 0.15
rpoA 3878046 c.462T>C synonymous_variant 0.19
rpoA 3878067 c.441C>G synonymous_variant 0.12
rpoA 3878070 c.438T>C synonymous_variant 0.15
rpoA 3878082 c.426T>G synonymous_variant 0.15
clpC1 4038596 c.2109A>G synonymous_variant 0.19
clpC1 4038623 c.2082A>G synonymous_variant 0.16
clpC1 4038662 c.2043T>C synonymous_variant 0.12
clpC1 4038671 c.2034T>G synonymous_variant 0.12
clpC1 4038695 c.2010C>G synonymous_variant 0.14
clpC1 4038701 c.2004G>C synonymous_variant 0.13
clpC1 4038704 c.2001T>C synonymous_variant 0.12
clpC1 4038713 c.1992T>C synonymous_variant 0.12
clpC1 4038740 c.1965G>C synonymous_variant 0.12
clpC1 4038755 c.1950G>C synonymous_variant 0.12
clpC1 4038773 c.1932T>C synonymous_variant 0.14
embC 4240548 p.Leu229Pro missense_variant 0.13
embC 4240619 p.Thr253Pro missense_variant 0.2
embC 4240831 c.969T>G synonymous_variant 0.12
embC 4242197 c.2337delC frameshift_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.96
embA 4244772 p.Ser514Pro missense_variant 0.33
embA 4244960 c.1728A>G synonymous_variant 0.25
embA 4244978 c.1746G>C synonymous_variant 0.33
embA 4244980 p.Val583Ala missense_variant 0.33
embA 4244982 c.1750T>C synonymous_variant 0.33
embA 4244987 c.1755T>C synonymous_variant 0.33
embA 4244994 p.Thr588Ser missense_variant 0.22
embA 4245003 p.Thr591Ala missense_variant 0.27
embA 4245008 c.1776T>C synonymous_variant 0.27
embA 4245014 c.1782C>G synonymous_variant 0.27
embA 4245020 c.1788T>C synonymous_variant 0.23
embA 4245023 c.1791A>G synonymous_variant 0.23
embA 4245026 c.1794T>C synonymous_variant 0.23
embA 4245029 c.1797T>C synonymous_variant 0.27
embA 4245032 c.1800A>C synonymous_variant 0.27
embA 4245041 c.1809C>G synonymous_variant 0.27
embA 4245053 c.1821G>C synonymous_variant 0.27
embA 4245059 c.1827G>C synonymous_variant 0.18
embA 4245060 c.1828T>C synonymous_variant 0.18
embA 4245077 c.1845G>C synonymous_variant 0.22
embA 4245083 c.1851A>G synonymous_variant 0.29
embA 4245093 p.Ile621Val missense_variant 0.29
embA 4245101 c.1869G>C synonymous_variant 0.29
embA 4245131 c.1899G>C synonymous_variant 0.25
embA 4245224 p.Tyr664* stop_gained 0.25
embA 4245328 c.2097delA frameshift_variant 0.17
embA 4245335 c.2103A>G synonymous_variant 0.14
embA 4245345 p.Met705Leu missense_variant 0.23
embA 4245355 p.Ala708Gly missense_variant 0.14
embA 4245359 c.2127G>C synonymous_variant 0.14
embA 4245362 c.2130G>C synonymous_variant 0.13
embB 4245714 c.-800C>T upstream_gene_variant 0.29
embB 4246164 c.-350T>C upstream_gene_variant 0.14
embA 4246173 p.Ile981Val missense_variant 0.17
embB 4246178 c.-336G>C upstream_gene_variant 0.17
embB 4246184 c.-330A>C upstream_gene_variant 0.17
embB 4246196 c.-318C>G upstream_gene_variant 0.17
embB 4246205 c.-309A>G upstream_gene_variant 0.17
embB 4246208 c.-306G>C upstream_gene_variant 0.17
embB 4246211 c.-303T>C upstream_gene_variant 0.17
embB 4246217 c.-297G>A upstream_gene_variant 0.17
embB 4246220 c.-294T>C upstream_gene_variant 0.17
embB 4246226 c.-288C>G upstream_gene_variant 0.17
embA 4246227 p.Ile999Val missense_variant 0.17
embB 4246235 c.-279G>A upstream_gene_variant 0.2
embB 4246250 c.-264G>C upstream_gene_variant 0.2
embB 4246259 c.-255G>C upstream_gene_variant 0.2
embB 4246274 c.-240G>C upstream_gene_variant 0.2
embB 4246825 p.Lys104Asn missense_variant 0.25
embB 4247738 p.Ala409Pro missense_variant 1.0
embB 4247793 p.Arg427Gln missense_variant 0.13
aftB 4268540 c.295_296delAT frameshift_variant 0.17
ubiA 4270022 c.-189C>A upstream_gene_variant 0.15
ethA 4326842 p.Tyr211Ser missense_variant 1.0
ethR 4327705 c.160_161delGC frameshift_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407861 c.342C>A synonymous_variant 0.12