TB-Profiler result

Run: SRR11972169
Summary

Run ID: SRR11972169

Sample name:

Date: 03-04-2023 05:30:30

Number of reads: 507019

Percentage reads mapped: 98.29

Strain: lineage2.2

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
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 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
gyrB 6230 p.Tyr331His missense_variant 0.12
gyrA 6478 c.-824G>A upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9016 p.Thr572Asn missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491281 p.Asp167Tyr missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760601 c.795C>T synonymous_variant 0.22
rpoB 760645 p.Pro280His missense_variant 0.2
rpoB 762275 c.2469C>A synonymous_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763426 c.57C>T synonymous_variant 0.18
rpoC 764058 p.Ala230Val missense_variant 1.0
rpoC 764916 p.Leu516Pro missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775883 p.Ile866Leu missense_variant 0.25
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777083 p.Asn466Lys missense_variant 0.18
mmpL5 777406 p.Ala359Thr missense_variant 0.18
mmpR5 779158 p.Ala57Thr missense_variant 0.15
mmpL5 779175 c.-695G>A upstream_gene_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303217 p.Arg96Gln missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472193 n.348A>G non_coding_transcript_exon_variant 0.18
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.26
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.38
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.27
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.24
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.23
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.23
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.21
rrs 1472350 n.505C>T non_coding_transcript_exon_variant 0.23
rrs 1472373 n.528G>A non_coding_transcript_exon_variant 0.14
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.15
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.12
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.13
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.13
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.13
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.12
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.21
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.15
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.15
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.15
rrl 1474737 n.1080G>T non_coding_transcript_exon_variant 0.17
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.16
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.16
fabG1 1673380 c.-60C>G upstream_gene_variant 0.32
inhA 1674727 c.527delC frameshift_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102665 c.377dupT frameshift_variant 0.22
ndh 2103060 c.-18C>T upstream_gene_variant 0.12
katG 2154331 p.Phe594Ser missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155449 c.663C>T synonymous_variant 0.17
PPE35 2167814 c.2799C>T synonymous_variant 0.25
PPE35 2167838 c.2775T>C synonymous_variant 0.22
PPE35 2167865 c.2748G>C synonymous_variant 0.2
PPE35 2167868 c.2745A>C synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.16
PPE35 2169935 p.Asn226Lys missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.57
PPE35 2170053 p.Thr187Ser missense_variant 0.57
PPE35 2170147 p.Ser156Ala missense_variant 0.17
PPE35 2170565 p.Phe16Leu missense_variant 0.11
Rv1979c 2221726 p.Thr480Asn missense_variant 0.15
Rv1979c 2222948 p.Arg73* stop_gained 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714454 c.879C>T synonymous_variant 0.18
ahpC 2726338 p.Val49Gly missense_variant 0.38
ahpC 2726341 p.Val50Gly missense_variant 0.57
ahpC 2726350 p.Trp53Leu missense_variant 0.2
folC 2747437 p.Met54Ile missense_variant 1.0
pepQ 2860063 p.Thr119Ile missense_variant 0.33
pepQ 2860330 p.Val30Ala missense_variant 0.15
pepQ 2860516 c.-98T>G upstream_gene_variant 0.13
Rv2752c 3065779 p.Val138Ala missense_variant 0.22
thyA 3074411 p.Arg21Cys missense_variant 0.2
thyA 3074580 c.-109T>C upstream_gene_variant 0.22
thyA 3074604 c.-133G>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612976 c.140delG frameshift_variant 0.2
Rv3236c 3613099 c.18G>A synonymous_variant 0.2
fbiB 3640776 c.-759C>T upstream_gene_variant 0.15
alr 3841539 c.-119C>T upstream_gene_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.19
clpC1 4039161 p.His515Gly missense_variant 0.18
clpC1 4039169 p.Glu512Asp missense_variant 0.17
clpC1 4039717 p.Lys330Glu missense_variant 0.2
clpC1 4039730 c.975C>G synonymous_variant 0.33
clpC1 4040057 c.648C>T synonymous_variant 0.33
clpC1 4040273 c.432T>A synonymous_variant 0.2
embC 4241958 p.Arg699Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.42
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4247784 p.Arg424Gln missense_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
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