TB-Profiler result

Run: SRR6964558
Summary

Run ID: SRR6964558

Sample name:

Date: 2024-10-03T22:54:57.259087

Number of reads: 4423057

Percentage reads mapped: 99.37

Median coverage: 99.0

Strain: lineage1.1.2;lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.1
lineage2 East-Asian RD105 0.88
lineage1.1 Indo-Oceanic RD239 0.07
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.91
lineage2.2 East-Asian (Beijing) RD105;RD207 0.89
lineage1 Indo-Oceanic RD239 0.05
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Phe Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Tyr34Ser Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
rpoB 761109 p.Asp435Phe missense_variant 0.87 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.93 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.89 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.9 isoniazid Assoc w R High-level resistance
pncA 2289141 p.Tyr34Ser missense_variant 0.86 pyrazinamide Assoc w R - Interim
embB 4247429 p.Met306Val missense_variant 0.97 ethambutol Assoc w R
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 Drugs Confidence
gyrB 6112 p.Met291Ile missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.14 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7655 c.354G>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8452 p.Ala384Val missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.13 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.94 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.95 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.86 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.85 ethionamide Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.11 rifampicin Not assoc w R
rpoB 759916 p.Lys37Arg missense_variant 0.93 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.19 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.2 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.89 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.12 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpL5 776690 c.1791C>T synonymous_variant 0.89 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.94 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.13 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303051 p.Val41Met missense_variant 0.15 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.92 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.21 ethambutol Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.1 capreomycin Uncertain significance
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.84 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.15 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.18 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.11 capreomycin Not assoc w R
Rv2752c 3065596 p.Leu199Ser missense_variant 0.86 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066009 c.183G>A synonymous_variant 0.95 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.93 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.92 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627907 c.-558C>T upstream_gene_variant 0.94 rifampicin
bedaquiline
alr 3840710 c.711A>G synonymous_variant 0.88 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.18 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.95 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.15 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.93 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.13 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.13 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.13 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.9 streptomycin Not assoc w R