TB-Profiler result

Run: SRR5526917
Summary

Run ID: SRR5526917

Sample name:

Date: 04-04-2023 10:36:24

Number of reads: 517843

Percentage reads mapped: 99.69

Strain: lineage2.2.1.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674262 p.Ile21Val missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg 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
gyrB 5861 c.623delT frameshift_variant 0.22
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 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762177 p.Arg791Ser missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763224 p.Glu1140Lys missense_variant 0.11
rpoC 763978 c.609C>A synonymous_variant 0.12
rpoC 764224 p.Lys285Asn missense_variant 0.13
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775807 p.Met892Val missense_variant 0.12
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
rpsL 781718 c.159C>T synonymous_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471938 n.93T>C non_coding_transcript_exon_variant 0.21
rrs 1472120 n.275G>T non_coding_transcript_exon_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
inhA 1673868 c.-334C>T upstream_gene_variant 0.2
inhA 1674698 p.Ser166Ile missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102738 c.304delG frameshift_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518390 c.276A>T synonymous_variant 0.18
kasA 2518562 p.Ala150Thr missense_variant 0.25
eis 2714846 p.Val163Ile missense_variant 1.0
Rv2752c 3065179 p.Ser338Leu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087846 p.Leu343Ile missense_variant 0.12
fprA 3473977 c.-30C>T upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612974 p.Ile48Thr missense_variant 0.17
fbiA 3640744 c.205delC frameshift_variant 0.13
fbiB 3642385 p.Leu284Arg missense_variant 0.13
rpoA 3877620 p.Glu296Asp missense_variant 0.12
clpC1 4039420 p.Ala429Ser missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245040 p.Leu603Pro missense_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248460 c.1947C>A synonymous_variant 0.12
aftB 4266984 p.Pro618Leu missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338552 c.-31A>C upstream_gene_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