TB-Profiler result

Run: SRR26936983
Summary

Run ID: SRR26936983

Sample name:

Date: 2024-10-04T17:14:37.503982

Number of reads: 981149

Percentage reads mapped: 98.13

Median coverage: 35.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 0.86
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr 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 embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met1000Arg Uncertain significance Mutation from literature
pyrazinamide pncA c.390_391dupGG Assoc w R
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 761139 p.His445Tyr missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 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 1.0 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 1.0 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4249512 p.Met1000Arg missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
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
dnaA 697 p.Arg233Trp missense_variant 1.0 isoniazid Uncertain significance
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin 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
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763675 c.306C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763703 c.334_336delTCGinsAGC synonymous_variant 0.16 rifampicin
rpoC 763709 c.340C>T synonymous_variant 0.16 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763726 c.357C>T synonymous_variant 0.15 rifampicin
rpoC 763771 c.402C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763780 c.411C>G synonymous_variant 0.16 rifampicin
rpoC 763792 p.Glu141Asp missense_variant 0.17 rifampicin
rpoC 763851 p.Ala161Gly missense_variant 0.13 rifampicin
rpoC 763858 c.489A>G synonymous_variant 0.14 rifampicin
rpoC 763872 p.Gly168Ala missense_variant 0.17 rifampicin
rpoC 763876 p.Glu169Asp missense_variant 0.18 rifampicin
rpoC 763879 c.510A>G synonymous_variant 0.17 rifampicin
rpoC 763888 c.519G>C synonymous_variant 0.2 rifampicin
rpoC 763891 c.522G>C synonymous_variant 0.18 rifampicin
rpoC 763894 c.525A>G synonymous_variant 0.18 rifampicin
rpoC 767134 c.3765C>A synonymous_variant 0.15 rifampicin
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
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin 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
Rv1258c 1406165 c.1176G>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472445 n.601_604delTCTC non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472451 n.606_607insCGGG non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472460 n.615T>C non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472461 n.616G>C non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472463 n.618G>C non_coding_transcript_exon_variant 0.15 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472489 n.644A>G non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
inhA 1673526 c.-676G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
ethionamide
rpsA 1833661 c.120A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834297 c.756C>T synonymous_variant 0.15 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834336 c.795C>G synonymous_variant 0.12 pyrazinamide
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 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726636 c.444G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv2681 2997224 c.486C>T synonymous_variant 1.0 capreomycin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.98 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv3236c 3613765 c.-649C>T upstream_gene_variant 1.0 pyrazinamide
lpqB 3623861 c.1050C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877656 c.852T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877677 p.Ala277Ser missense_variant 0.15 rifampicin
rpoA 3877680 c.828G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877686 c.822A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877737 c.771G>C synonymous_variant 0.23 rifampicin
rpoA 3877758 c.750G>C synonymous_variant 0.18 rifampicin
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.96 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 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 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 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R