TB-Profiler result

Run: ERR5864460
Summary

Run ID: ERR5864460

Sample name:

Date: 01-04-2023 23:21:44

Number of reads: 2153017

Percentage reads mapped: 99.57

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
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
gyrA 7563 p.Gly88Cys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
tlyA 1918665 c.728dupT frameshift_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289030 p.His71Arg missense_variant 1.0 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.96 ethambutol
embB 4247513 p.Tyr334His missense_variant 1.0 ethambutol
ethA 4326800 c.672_673dupGC frameshift_variant 0.15 ethionamide, ethionamide
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 5593 c.354T>C synonymous_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9759 p.Glu820Lys missense_variant 0.1
fgd1 491012 p.Pro77His missense_variant 0.22
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 760089 p.Gly95Arg missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765668 p.His767Asn missense_variant 0.1
rpoC 766222 c.2853T>C synonymous_variant 0.12
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303078 p.Ala50Thr missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.307delC non_coding_transcript_exon_variant 0.13
rrl 1473969 n.312G>T non_coding_transcript_exon_variant 0.12
rrl 1473970 n.313G>T non_coding_transcript_exon_variant 0.12
rrl 1475445 n.1788T>G non_coding_transcript_exon_variant 0.12
fabG1 1674029 p.Arg197Gln missense_variant 0.12
inhA 1674777 c.576C>T synonymous_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834892 c.1353delC frameshift_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102371 c.671delT frameshift_variant 0.96
ndh 2102845 c.198A>T synonymous_variant 0.13
katG 2154646 p.Arg489His missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170241 c.372C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290007 c.-766A>T upstream_gene_variant 0.11
kasA 2518147 c.33C>T synonymous_variant 0.3
eis 2714579 c.754T>C synonymous_variant 0.12
ahpC 2726549 p.Ser119Arg missense_variant 0.1
pepQ 2859506 p.Ala305Thr missense_variant 0.13
pepQ 2860162 p.Arg86Pro missense_variant 0.1
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ribD 2986976 c.138C>T synonymous_variant 0.12
thyX 3067283 c.663C>T synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087532 p.Ala238Asp missense_variant 1.0
fbiD 3338994 c.-124G>C upstream_gene_variant 0.11
Rv3083 3448437 c.-67C>T upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641265 c.-270C>A upstream_gene_variant 0.11
fbiB 3641540 c.6C>A synonymous_variant 0.11
clpC1 4038242 c.2463C>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244604 p.Val458Met missense_variant 0.2
embB 4248630 c.2119dupG frameshift_variant 0.11
embB 4249707 p.Arg1065Leu missense_variant 0.15
embB 4249752 p.Leu1080Ser missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268500 p.Arg113Cys missense_variant 0.12
aftB 4269459 c.-623G>T upstream_gene_variant 0.11
ubiA 4269793 c.40delG frameshift_variant 0.12
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