TB-Profiler result

Run: SRR11972462
Summary

Run ID: SRR11972462

Sample name:

Date: 03-04-2023 05:43:50

Number of reads: 636330

Percentage reads mapped: 98.22

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 0.98
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
gyrB 5312 p.Ala25Thr missense_variant 0.12
gyrB 5727 p.Pro163Gln missense_variant 0.18
gyrB 5825 p.Glu196* stop_gained 0.12
gyrB 6078 p.Gly280Val missense_variant 0.2
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 491718 c.936A>T synonymous_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575442 p.Gly32Glu missense_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620865 c.975A>G stop_lost&splice_region_variant 0.17
rpoB 761680 p.Glu625Gly missense_variant 0.4
rpoB 761981 c.2175C>T synonymous_variant 0.2
rpoB 762086 c.2280G>A synonymous_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764278 c.909A>G synonymous_variant 0.15
rpoC 765365 p.Thr666Ala missense_variant 0.5
rpoC 766316 p.Met983Val missense_variant 0.18
rpoC 767126 p.Ile1253Val missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775715 c.2766G>A synonymous_variant 0.15
mmpL5 775718 c.2763C>G synonymous_variant 0.17
mmpL5 775726 c.2755C>T synonymous_variant 0.17
mmpL5 775727 c.2754C>G synonymous_variant 0.17
mmpL5 775751 c.2730C>T synonymous_variant 0.13
mmpL5 776010 c.2470delC frameshift_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 0.18
mmpL5 778303 p.Gln60Lys missense_variant 0.15
mmpS5 778884 p.Ala8Ser missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303280 p.Gln117Arg missense_variant 0.11
fbiC 1304758 p.Pro610Ser missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417466 c.-119T>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917833 c.-107G>T upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101790 p.Thr418Met missense_variant 0.2
ndh 2102155 c.888G>A synonymous_variant 0.25
katG 2154567 c.1545C>A synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167833 p.Leu927Arg missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.14
PPE35 2169287 c.1326T>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.15
PPE35 2170053 p.Thr187Ser missense_variant 0.19
PPE35 2170808 c.-196G>A upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714526 c.805_806delAC frameshift_variant 1.0
eis 2715057 c.276C>T synonymous_variant 0.17
eis 2715060 p.His91Met missense_variant 0.18
eis 2715065 p.Thr90Ala missense_variant 0.18
folC 2746887 p.Val238Ile missense_variant 0.25
pepQ 2860595 c.-179_-178delAC upstream_gene_variant 0.13
Rv2752c 3065073 c.1119C>T synonymous_variant 0.14
Rv2752c 3065498 p.Arg232Trp missense_variant 0.13
Rv2752c 3065711 p.Gly161Ser missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474498 c.492G>A synonymous_variant 0.12
Rv3236c 3612734 p.Ser128Tyr missense_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641451 c.-84G>T upstream_gene_variant 0.17
fbiA 3641504 p.Arg321His missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.17
clpC1 4039714 p.Tyr331His missense_variant 0.12
clpC1 4039829 p.Leu292Ile missense_variant 0.13
clpC1 4040057 c.648C>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243054 c.-179G>T upstream_gene_variant 0.25
embA 4243206 c.-27T>A upstream_gene_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244447 c.1215G>T synonymous_variant 0.2
embB 4247470 c.957T>C synonymous_variant 0.22
embB 4247472 p.Phe320Tyr missense_variant 0.22
embB 4248834 p.Trp774* stop_gained 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268680 p.Glu53Lys missense_variant 0.29
ubiA 4269922 c.-89C>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0