TB-Profiler result

Run: SRR21277781

Summary

Run ID: SRR21277781

Sample name:

Date: 04-04-2023 01:40:58

Number of reads: 13001693

Percentage reads mapped: 95.42

Strain: lineage2.2.1.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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 2155733 p.Gln127* stop_gained 0.12 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9327 p.Ala676Thr missense_variant 0.11
fgd1 491308 p.Ala176Thr missense_variant 0.12
fgd1 491317 p.Pro179Thr missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575250 c.-98G>A upstream_gene_variant 0.12
mshA 575658 p.Ala104Glu missense_variant 0.18
mshA 575690 p.Gly115Trp missense_variant 0.18
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575925 p.Gly193Val missense_variant 0.2
mshA 576258 p.Ser304Ile missense_variant 0.15
mshA 576260 p.Gly305Cys missense_variant 0.12
mshA 576452 p.Val369Met missense_variant 0.33
ccsA 619704 c.-187G>A upstream_gene_variant 0.2
ccsA 619864 c.-27G>T upstream_gene_variant 0.15
ccsA 620256 c.366C>A synonymous_variant 0.12
ccsA 620297 p.Pro136Gln missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760458 p.Val218Leu missense_variant 0.11
rpoB 761182 p.Arg459His missense_variant 0.1
rpoB 761651 p.Ser615Arg missense_variant 0.13
rpoB 762652 p.Trp949* stop_gained 0.12
rpoC 762665 c.-705G>A upstream_gene_variant 0.12
rpoC 762668 c.-702C>A upstream_gene_variant 0.14
rpoB 762783 p.Asp993Tyr missense_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763885 c.516C>A synonymous_variant 0.12
rpoC 763954 c.585C>T synonymous_variant 0.12
rpoC 763957 p.Lys196Asn missense_variant 0.1
rpoC 763968 p.Gly200Val missense_variant 0.16
rpoC 764547 p.Gly393Glu missense_variant 0.1
rpoC 764601 p.Gly411Val missense_variant 0.1
rpoC 765287 p.Leu640Met missense_variant 0.12
rpoC 766042 p.Cys891* stop_gained 0.11
rpoC 766137 p.Arg923Leu missense_variant 0.11
rpoC 766482 p.Arg1038Leu missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777317 c.1164C>T synonymous_variant 0.22
mmpL5 777389 p.Phe364Leu missense_variant 0.19
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rplC 801235 p.Ala143Thr missense_variant 0.12
fbiC 1303135 p.Gly69Cys missense_variant 0.1
fbiC 1303934 p.Pro335Arg missense_variant 0.2
fbiC 1304488 p.Ala520Ser missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99
embR 1416485 p.Ala288Glu missense_variant 0.11
embR 1416959 p.Arg130Leu missense_variant 0.1
embR 1416966 p.Ala128Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917967 p.Glu10Lys missense_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 0.75
tlyA 1918555 c.616C>A synonymous_variant 0.12
tlyA 1918560 c.621G>A synonymous_variant 0.11
tlyA 1918566 c.627C>A synonymous_variant 0.22
tlyA 1918602 c.663C>T synonymous_variant 0.17
ndh 2101696 c.1347C>A synonymous_variant 0.11
ndh 2101700 p.Leu448Gln missense_variant 0.18
ndh 2102352 p.Arg231Trp missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155737 c.375C>T synonymous_variant 0.14
katG 2155743 c.369G>T synonymous_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170031 c.582C>T synonymous_variant 0.12
PPE35 2170342 p.Gln91* stop_gained 0.2
PPE35 2170514 c.99G>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518839 p.Ala242Val missense_variant 0.11
kasA 2519000 p.Glu296Lys missense_variant 0.12
eis 2714778 p.Gln185His missense_variant 0.1
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2714872 p.Pro154Lys missense_variant 0.14
folC 2746301 p.Ala433Val missense_variant 0.11
folC 2746374 p.Pro409Ser missense_variant 0.12
folC 2746581 p.Glu340* stop_gained 0.12
folC 2746582 p.Leu339Phe missense_variant 0.36
folC 2746637 p.Leu321His missense_variant 0.2
folC 2746908 p.Val231Ile missense_variant 0.11
folC 2747326 c.273G>T synonymous_variant 0.12
folC 2747329 c.270C>T synonymous_variant 0.13
folC 2747355 p.Val82Ile missense_variant 0.13
folC 2747792 c.-194G>A upstream_gene_variant 0.11
pepQ 2859592 p.Ala276Val missense_variant 0.17
pepQ 2859600 c.819G>T synonymous_variant 0.25
pepQ 2859623 p.Pro266Thr missense_variant 0.2
pepQ 2860232 p.Gln63Lys missense_variant 0.12
pepQ 2860589 c.-171G>T upstream_gene_variant 1.0
ribD 2986659 c.-180G>T upstream_gene_variant 0.12
ribD 2987302 p.Arg155Gln missense_variant 0.12
Rv2752c 3066336 c.-145C>A upstream_gene_variant 0.13
Rv2752c 3067191 c.-1000G>T upstream_gene_variant 0.1
thyX 3067553 c.393C>A synonymous_variant 0.17
thyX 3067561 p.Arg129Ser missense_variant 0.12
thyX 3067852 p.Gly32* stop_gained 0.1
thyX 3067856 c.90C>T synonymous_variant 0.17
thyX 3068008 c.-63G>A upstream_gene_variant 0.11
thyA 3074501 c.-30G>T upstream_gene_variant 0.12
thyA 3074520 c.-49G>T upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087338 c.519G>T synonymous_variant 0.18
ald 3087349 p.Gly177Val missense_variant 0.1
fbiD 3338934 c.-184C>A upstream_gene_variant 0.12
fbiD 3339318 c.201C>A synonymous_variant 0.1
fbiD 3339331 p.Ala72Thr missense_variant 0.2
fbiD 3339342 c.225G>T synonymous_variant 0.12
fbiD 3339555 c.438C>A synonymous_variant 0.18
Rv3083 3448333 c.-171G>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474912 c.906G>A synonymous_variant 0.17
fprA 3475297 c.1291C>A synonymous_variant 0.15
Rv3236c 3612140 p.Ala326Val missense_variant 0.12
Rv3236c 3612176 p.Arg314Gln missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
fbiA 3641377 p.Arg279Trp missense_variant 0.15
fbiB 3641463 c.-72G>T upstream_gene_variant 0.12
fbiB 3641643 p.Ala37Ser missense_variant 0.13
fbiB 3641875 p.Gly114Asp missense_variant 0.12
fbiB 3641907 p.Pro125Thr missense_variant 0.33
fbiB 3642164 c.630C>A synonymous_variant 0.11
fbiB 3642394 p.Pro287Leu missense_variant 0.12
fbiB 3642665 c.1131C>A synonymous_variant 0.27
fbiB 3642724 p.Trp397Leu missense_variant 0.11
alr 3841226 c.195C>A synonymous_variant 0.11
ddn 3986649 c.-195G>T upstream_gene_variant 0.13
clpC1 4040244 p.Gly154Val missense_variant 0.15
embC 4240642 c.780G>T synonymous_variant 0.13
embC 4241209 c.1347G>A synonymous_variant 0.14
embC 4241259 p.Arg466Leu missense_variant 0.17
embC 4241692 c.1830C>T synonymous_variant 0.11
embC 4242176 p.Pro772Ser missense_variant 0.33
embA 4242328 c.-905C>A upstream_gene_variant 0.14
embA 4242340 c.-893C>A upstream_gene_variant 0.11
embC 4242369 p.Arg836His missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243479 p.Pro83Thr missense_variant 0.14
embA 4243978 p.Ala249Val missense_variant 0.13
embA 4244205 p.Arg325Ser missense_variant 0.16
embA 4244860 p.Gly543Val missense_variant 0.12
embA 4244864 c.1632G>A synonymous_variant 0.13
embA 4245418 p.Gly729Glu missense_variant 0.11
embA 4245512 c.2280G>T synonymous_variant 0.15
embA 4245516 p.Gly762* stop_gained 0.11
embB 4245713 c.-801G>T upstream_gene_variant 0.18
embB 4245818 c.-696C>T upstream_gene_variant 0.14
embB 4246800 p.Gly96Val missense_variant 0.25
embB 4246808 c.295C>T synonymous_variant 0.11
embB 4247005 c.492C>A synonymous_variant 0.22
embB 4247152 c.639G>T synonymous_variant 0.15
embB 4247171 c.658C>T synonymous_variant 0.11
embB 4247621 p.Leu370Ile missense_variant 0.1
embB 4247660 p.Ala383Ser missense_variant 0.14
embB 4247794 c.1281G>A synonymous_variant 0.12
embB 4247799 p.Thr429Lys missense_variant 0.17
embB 4247802 p.Pro430Gln missense_variant 0.25
embB 4247916 p.Arg468His missense_variant 0.17
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248583 c.2070C>A synonymous_variant 0.11
embB 4248586 c.2073C>A synonymous_variant 0.14
embB 4248589 c.2076C>A synonymous_variant 0.14
embB 4248603 p.Arg697Leu missense_variant 0.22
embB 4249360 c.2847G>T synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267687 p.Gly384Ser missense_variant 0.12
aftB 4267689 p.Ala383Glu missense_variant 0.11
aftB 4267904 c.933G>T synonymous_variant 0.12
aftB 4267962 p.Pro292His missense_variant 0.18
aftB 4267970 p.Phe289Leu missense_variant 0.15
aftB 4268255 c.582G>T synonymous_variant 0.12
aftB 4268870 c.-34G>T upstream_gene_variant 0.33
aftB 4268888 c.-52C>A upstream_gene_variant 0.13
aftB 4268889 c.-53C>A upstream_gene_variant 0.11
aftB 4268905 c.-69C>A upstream_gene_variant 0.12
aftB 4269708 c.-872C>T upstream_gene_variant 0.11
ubiA 4269725 p.Leu37Met missense_variant 0.12
aftB 4269726 c.-890G>T upstream_gene_variant 0.12
aftB 4269735 c.-899G>A upstream_gene_variant 0.14
ethR 4326889 c.-660C>A upstream_gene_variant 0.1
ethA 4327599 c.-126G>T upstream_gene_variant 0.12
ethA 4328023 c.-550G>T upstream_gene_variant 0.16
ethA 4328417 c.-944G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408148 p.Ala19Thr missense_variant 0.12