TB-Profiler result

Run: SRR11972158
Summary

Run ID: SRR11972158

Sample name:

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

Number of reads: 475161

Percentage reads mapped: 98.74

Strain: lineage2.2

Drug-resistance: MDR-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
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289226 c.15dupC frameshift_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4247496 p.Asp328Gly missense_variant 1.0 ethambutol
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 8849 c.1548C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620085 c.195G>A synonymous_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764058 p.Ala230Val missense_variant 1.0
rpoC 764321 p.Pro318Ser missense_variant 1.0
rpoC 764496 p.Glu376Val missense_variant 0.17
rpoC 765839 p.Val824Met missense_variant 0.2
rpoC 766232 p.Ala955Ser missense_variant 0.15
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 776770 p.Ile571Val missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801038 p.Pro77Arg missense_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471861 n.16T>C non_coding_transcript_exon_variant 1.0
rrs 1471965 n.120T>C non_coding_transcript_exon_variant 0.12
rrl 1473848 n.191G>C non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.25
fabG1 1673349 c.-91G>C upstream_gene_variant 0.25
fabG1 1673357 c.-83G>A upstream_gene_variant 0.21
fabG1 1673359 c.-81T>C upstream_gene_variant 0.25
fabG1 1673361 c.-79C>G upstream_gene_variant 0.25
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101749 p.Thr432Ala missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.17
PPE35 2167868 c.2745A>C synonymous_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.22
PPE35 2170528 p.Ser29Ala missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746708 p.His297Gln missense_variant 0.25
folC 2747437 p.Met54Ile missense_variant 1.0
ribD 2987009 c.171C>A synonymous_variant 0.4
Rv2752c 3064822 c.1349_1369delACGGCTTGATCGCCGGCGACG disruptive_inframe_deletion 0.25
Rv2752c 3066386 c.-195C>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087879 p.Arg354Trp missense_variant 0.15
fbiD 3339273 c.156T>G synonymous_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642040 p.Gly169Asp missense_variant 0.22
fbiB 3642199 p.Val222Ala missense_variant 0.33
clpC1 4039664 c.1041G>C synonymous_variant 0.14
clpC1 4039667 p.Gln346Tyr missense_variant 0.14
clpC1 4039674 p.Pro344Gln missense_variant 0.18
clpC1 4039676 c.1029G>A synonymous_variant 0.18
clpC1 4039682 c.1023C>T synonymous_variant 0.18
clpC1 4039691 c.1014G>C synonymous_variant 0.17
clpC1 4040828 c.-124T>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243082 c.3221_3228delATCTGAAC frameshift_variant 0.33
embC 4243092 p.Leu1077Arg missense_variant 0.3
embC 4243095 p.Gly1078Val missense_variant 0.3
embA 4243099 c.-134G>C upstream_gene_variant 0.3
embA 4243102 c.-131G>T upstream_gene_variant 0.3
embC 4243103 p.Thr1081Pro missense_variant 0.3
embC 4243106 p.Arg1082Ser missense_variant 0.3
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.3
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244184 p.Ser318Arg missense_variant 0.12
embA 4245082 p.Ala617Val missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.27
embB 4246548 p.Pro12Gln missense_variant 0.31
embB 4246555 c.42G>C synonymous_variant 0.33
embB 4246556 p.Ala15Pro missense_variant 0.33
embB 4246563 p.Leu17Trp missense_variant 0.27
embB 4246567 c.54G>T synonymous_variant 0.25
embB 4247529 p.Leu339Pro missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4270025 c.-193_-192insGTGGTC upstream_gene_variant 0.17
ethA 4328357 c.-884A>T upstream_gene_variant 0.25
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 4407934 p.Leu90Arg missense_variant 1.0