TB-Profiler result

Run: SRR21277518

Summary

Run ID: SRR21277518

Sample name:

Date: 04-04-2023 01:19:33

Number of reads: 9084015

Percentage reads mapped: 96.16

Strain: lineage2.2.1

Drug-resistance: Sensitive


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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
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
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 491317 p.Pro179Thr missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575521 c.174A>T synonymous_variant 0.11
mshA 575781 p.Pro145Leu missense_variant 0.12
mshA 575920 c.573C>T synonymous_variant 0.22
mshA 575923 c.576C>T synonymous_variant 0.1
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761645 c.1839C>A synonymous_variant 0.12
rpoB 761652 p.Glu616Lys missense_variant 0.17
rpoB 761692 p.Ala629Val missense_variant 0.14
rpoC 762788 c.-582G>T upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763906 c.537C>A synonymous_variant 0.11
rpoC 763952 p.Arg195Cys missense_variant 0.38
rpoC 763957 p.Lys196Asn missense_variant 0.12
rpoC 763968 p.Gly200Val missense_variant 0.12
rpoC 764549 p.Pro394Thr missense_variant 0.12
rpoC 764596 p.Lys409Asn missense_variant 0.1
rpoC 765304 p.Glu645Asp missense_variant 0.12
rpoC 766137 p.Arg923Leu missense_variant 0.11
rpoC 766144 c.2775G>T synonymous_variant 0.12
rpoC 766969 c.3600C>A synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777650 c.831C>T synonymous_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801236 p.Ala143Glu missense_variant 0.15
rplC 801257 p.Ser150Phe missense_variant 0.13
fbiC 1303093 p.Leu55Met missense_variant 0.17
fbiC 1303914 c.984C>A synonymous_variant 0.15
fbiC 1304102 p.Arg391Gln missense_variant 0.22
fbiC 1304311 p.Ala461Ser missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
embR 1416983 p.Gly122Asp missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673172 c.-268T>G upstream_gene_variant 1.0
inhA 1674811 p.Gly204Ser missense_variant 0.13
inhA 1674856 p.Glu219* stop_gained 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918305 c.366G>A synonymous_variant 0.2
ndh 2101679 p.Ser455Leu missense_variant 0.11
ndh 2102207 p.Gly279Val missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155747 p.Ala122Val missense_variant 0.33
katG 2155772 p.Arg114Ser missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170089 p.Pro175Gln missense_variant 1.0
PPE35 2170349 c.264C>T synonymous_variant 0.12
PPE35 2170520 p.Trp31* stop_gained 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518798 c.684G>T synonymous_variant 0.2
eis 2715036 c.297G>T synonymous_variant 0.29
eis 2715058 p.Arg92His missense_variant 0.29
eis 2715076 p.Ala86Glu missense_variant 0.12
folC 2746287 p.Asp438Tyr missense_variant 0.11
folC 2746384 p.His405Gln missense_variant 0.12
folC 2746636 c.963C>A synonymous_variant 0.29
folC 2747349 p.Ala84Thr missense_variant 0.11
pepQ 2859592 p.Ala276Val missense_variant 0.12
pepQ 2859605 p.Gly272Trp missense_variant 0.21
pepQ 2859611 p.Leu270Met missense_variant 0.2
pepQ 2859962 p.Ala153Thr missense_variant 0.12
pepQ 2860125 p.Glu98Asp missense_variant 0.15
pepQ 2860142 p.Gly93Arg missense_variant 1.0
pepQ 2860232 p.Gln63Lys missense_variant 0.11
pepQ 2860589 c.-171G>T upstream_gene_variant 1.0
ribD 2986762 c.-77G>A upstream_gene_variant 1.0
ribD 2987501 c.663C>T synonymous_variant 0.17
Rv2752c 3066275 c.-84G>T upstream_gene_variant 0.11
Rv2752c 3067024 c.-833C>A upstream_gene_variant 0.13
thyX 3067400 c.546C>T synonymous_variant 0.22
thyX 3067541 c.405C>A synonymous_variant 0.43
thyX 3067846 p.Ala34Ser missense_variant 0.11
thyA 3074522 c.-51C>A upstream_gene_variant 0.1
thyA 3074536 c.-65G>A upstream_gene_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339342 c.225G>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612148 p.Gln323His missense_variant 0.11
Rv3236c 3612162 p.Ala319Ser missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97
fbiA 3641356 p.Val272Met missense_variant 0.12
fbiB 3641640 p.Ala36Ser missense_variant 0.12
fbiB 3641882 c.348C>A synonymous_variant 0.11
fbiB 3642039 p.Gly169Cys missense_variant 0.2
fbiB 3642174 p.Val214Met missense_variant 0.17
fbiB 3642394 p.Pro287Leu missense_variant 0.12
fbiB 3642656 c.1122G>A synonymous_variant 0.12
rpoA 3878584 c.-77C>T upstream_gene_variant 0.11
clpC1 4039805 c.900C>T synonymous_variant 1.0
clpC1 4040253 p.Ala151Asp missense_variant 0.18
embC 4240653 p.Pro264Leu missense_variant 0.15
embC 4240981 c.1119G>A synonymous_variant 0.1
embA 4242340 c.-893C>A upstream_gene_variant 0.11
embC 4242351 p.Pro830Gln missense_variant 0.29
embC 4242607 p.Met915Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243190 c.-43G>T upstream_gene_variant 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243630 p.Ala133Val missense_variant 0.2
embA 4243866 p.Leu212Met missense_variant 0.11
embA 4243967 c.735G>T synonymous_variant 0.14
embA 4244213 c.981C>A synonymous_variant 0.17
embA 4244436 p.Leu402Ile missense_variant 0.15
embA 4244851 p.Arg540Gln missense_variant 0.18
embA 4244941 p.Trp570Leu missense_variant 0.12
embA 4245468 p.Asn746Tyr missense_variant 0.14
embA 4245660 p.Ala810Thr missense_variant 0.11
embA 4246024 p.Trp931Leu missense_variant 0.14
embB 4246584 p.Arg24Pro missense_variant 0.19
embB 4247015 p.Ser168Thr missense_variant 0.14
embB 4247626 c.1113C>A synonymous_variant 0.43
embB 4247803 c.1290G>A synonymous_variant 0.15
embB 4248591 p.Ala693Asp missense_variant 0.17
embB 4248624 p.Thr704Ile missense_variant 0.15
embB 4249168 c.2655C>A synonymous_variant 0.11
embB 4249180 c.2667G>A synonymous_variant 0.13
embB 4249345 c.2832C>A synonymous_variant 0.15
embB 4249353 p.Arg947Leu missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267911 p.Pro309Leu missense_variant 0.12
aftB 4268249 c.588G>T synonymous_variant 0.17
aftB 4268306 p.Phe177Leu missense_variant 0.11
aftB 4268505 p.Arg111Leu missense_variant 0.11
ethA 4326676 p.Ser266Arg missense_variant 1.0
ethR 4328030 p.Ala161Glu missense_variant 0.15
ethR 4328048 p.Pro167Leu missense_variant 0.2
whiB6 4338337 p.Cys62Tyr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338665 c.-144C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407927 p.Glu92Asp missense_variant 1.0