TB-Profiler result

Run: SRR21277803
Summary

Run ID: SRR21277803

Sample name:

Date: 04-04-2023 01:44:09

Number of reads: 14936507

Percentage reads mapped: 98.05

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 491742 c.960T>C synonymous_variant 1.0
mshA 575407 c.60C>A synonymous_variant 0.12
mshA 575500 c.153G>T synonymous_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576253 c.906G>T synonymous_variant 0.12
mshA 576449 p.Pro368Lys missense_variant 0.12
mshA 576577 c.1230C>A synonymous_variant 0.18
mshA 576609 p.Ala421Val missense_variant 0.11
ccsA 619713 c.-178C>A upstream_gene_variant 0.13
ccsA 619723 c.-168G>A upstream_gene_variant 0.27
ccsA 619813 c.-78C>T upstream_gene_variant 0.25
ccsA 619977 c.87G>A synonymous_variant 0.11
ccsA 619998 p.Phe36Leu missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761658 p.Pro618Thr missense_variant 0.12
rpoB 762678 p.Leu958Ile missense_variant 0.14
rpoB 762684 p.Ala960Thr missense_variant 0.14
rpoB 762775 p.Arg990Leu missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763926 p.Ala186Asp missense_variant 0.15
rpoC 766967 p.Pro1200Thr missense_variant 0.14
rpoC 766970 p.Ala1201Thr missense_variant 0.27
rpoC 766976 p.Gly1203Cys missense_variant 0.29
rpoC 766979 p.Arg1204Cys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777362 p.Met373Ile missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303122 c.192G>T synonymous_variant 0.19
fbiC 1304457 c.1527C>T synonymous_variant 0.23
fbiC 1305450 c.2520C>A synonymous_variant 0.11
fbiC 1305452 p.Gly841Asp missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407165 p.Thr59Lys missense_variant 0.1
embR 1416974 p.Ala125Val missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674822 c.621C>A synonymous_variant 0.12
rpsA 1833410 c.-132G>A upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834865 p.Gly442Arg missense_variant 0.11
rpsA 1834870 c.1329C>A synonymous_variant 0.17
tlyA 1917964 p.Ala9Thr missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 0.83
tlyA 1918198 p.Leu87Met missense_variant 0.12
tlyA 1918570 p.Val211Ile missense_variant 0.12
tlyA 1918580 p.Arg214Leu missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155743 c.369G>T synonymous_variant 0.13
katG 2155760 p.Gly118Ser missense_variant 0.21
katG 2155763 p.Asp117Asn missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170097 c.516G>A synonymous_variant 0.25
PPE35 2170100 c.513G>A synonymous_variant 0.18
PPE35 2170354 p.Ala87Ser missense_variant 0.13
PPE35 2170357 p.Ala86Ser missense_variant 0.22
PPE35 2170520 p.Trp31* stop_gained 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519008 c.894C>A synonymous_variant 0.17
kasA 2519159 p.Ala349Ser missense_variant 0.12
eis 2714865 c.468C>T synonymous_variant 0.12
eis 2714868 c.465C>A synonymous_variant 0.12
eis 2715037 p.Ala99Val missense_variant 0.12
eis 2715042 c.291G>A synonymous_variant 0.19
folC 2746309 c.1290G>T synonymous_variant 0.11
folC 2746590 p.Gly337Cys missense_variant 0.11
pepQ 2859603 p.Gly272Cys missense_variant 0.12
pepQ 2859924 c.495G>T synonymous_variant 0.11
pepQ 2859940 p.Arg160His missense_variant 0.2
pepQ 2860150 p.Ala90Val missense_variant 0.12
pepQ 2860182 c.237C>T synonymous_variant 0.14
pepQ 2860589 c.-171G>T upstream_gene_variant 0.5
ribD 2987306 c.468C>A synonymous_variant 0.11
ribD 2987307 p.Ala157Thr missense_variant 0.1
ribD 2987315 c.477C>A synonymous_variant 0.2
Rv2752c 3066291 c.-100G>T upstream_gene_variant 0.14
Rv2752c 3066302 c.-111C>A upstream_gene_variant 0.1
thyX 3067200 p.Glu249Val missense_variant 0.12
thyX 3067212 p.Pro245Leu missense_variant 0.14
thyX 3067222 p.Ala242Ser missense_variant 0.5
thyX 3067297 p.Arg217Ser missense_variant 0.29
thyX 3067298 c.648G>A synonymous_variant 0.18
thyX 3067302 p.Cys215Tyr missense_variant 0.12
thyX 3067418 c.528C>T synonymous_variant 0.14
thyX 3067541 c.405C>A synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087302 c.483C>A synonymous_variant 0.11
ald 3087303 p.Gly162Arg missense_variant 0.14
ald 3087332 c.513C>T synonymous_variant 0.15
ald 3087333 p.Val172Leu missense_variant 0.11
fbiD 3339332 p.Ala72Glu missense_variant 0.11
fbiD 3339558 c.441C>A synonymous_variant 0.15
fbiD 3339729 c.612G>T synonymous_variant 0.22
fbiD 3339747 c.630G>T synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474921 c.915G>A synonymous_variant 0.12
fprA 3474926 p.Thr307Lys missense_variant 0.11
fprA 3474983 p.Gly326Val missense_variant 0.33
fprA 3474989 p.Pro328Leu missense_variant 0.14
fprA 3475312 p.Pro436Thr missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
fbiB 3641388 c.-147C>T upstream_gene_variant 0.12
fbiB 3641630 c.96C>T synonymous_variant 0.1
fbiB 3641907 p.Pro125Thr missense_variant 0.11
fbiB 3642173 c.639G>A synonymous_variant 0.14
fbiB 3642183 p.Val217Met missense_variant 0.18
fbiB 3642190 p.Gly219Glu missense_variant 0.25
fbiB 3642324 p.Arg264Ser missense_variant 0.11
fbiB 3642380 p.Glu282Asp missense_variant 0.15
alr 3840986 c.435G>T synonymous_variant 0.12
alr 3841003 p.Glu140* stop_gained 0.14
clpC1 4038195 p.Ala837Glu missense_variant 0.12
panD 4044480 c.-199G>T upstream_gene_variant 0.14
embC 4242362 p.Gly834Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242687 p.Gln942Leu missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243615 p.Arg128Leu missense_variant 0.18
embA 4243934 c.702C>T synonymous_variant 0.25
embA 4244221 p.Leu330Gln missense_variant 0.11
embA 4244291 c.1059G>T synonymous_variant 0.25
embA 4244447 c.1215G>A synonymous_variant 0.12
embA 4244867 c.1635C>A synonymous_variant 0.1
embA 4244909 c.1677C>T synonymous_variant 0.11
embA 4245452 c.2220G>A synonymous_variant 0.12
embA 4245454 p.Ala741Asp missense_variant 0.1
embA 4245461 c.2229C>A synonymous_variant 0.11
embB 4246798 c.285C>T synonymous_variant 0.17
embB 4247108 p.Gly199Cys missense_variant 0.25
embB 4247645 p.Glu378* stop_gained 0.18
embB 4248593 p.Gly694Ser missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267671 p.Ala389Glu missense_variant 0.12
aftB 4267919 p.Gln306His missense_variant 0.1
aftB 4267926 p.Ala304Val missense_variant 0.11
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