TB-Profiler result

Run: SRR1049962
Summary

Run ID: SRR1049962

Sample name:

Date: 2024-03-25T19:05:15.943675

Number of reads: 1764371

Percentage reads mapped: 98.21

Median coverage: 37.0

Strain: lineage4.1.3;lineage6.3.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.12
lineage4.1 Euro-American None 0.85
lineage6.3 West-Africa 2 RD702 0.13
lineage4 Euro-American None 0.9
lineage6.3.1 West-Africa 2 RD702 0.19
lineage6 West-Africa 2 RD702 0.21
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
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 6446 p.Ala403Ser missense_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 6507 p.Ala423Val missense_variant 0.68 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 6847 c.-455C>T upstream_gene_variant 0.77 levofloxacin
moxifloxacin
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
gyrA 9656 c.2355C>G synonymous_variant 0.69 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.24 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 619628 c.-263G>A upstream_gene_variant 0.26 capreomycin
amikacin
kanamycin
Rv0565c 657269 p.Ser68Pro missense_variant 0.82 ethionamide Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.88 rifampicin Not assoc w R
rpoC 765187 c.1818C>T synonymous_variant 0.79 rifampicin Not assoc w R - Interim
rpoC 766012 c.2643C>G synonymous_variant 0.65 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 775841 c.2640G>A synonymous_variant 0.28 clofazimine
bedaquiline
mmpL5 776100 p.Thr794Ile missense_variant 0.24 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 0.8 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.27 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406260 p.Pro361Ser missense_variant 0.81 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474739 n.1082G>A non_coding_transcript_exon_variant 0.56 capreomycin
linezolid
fabG1 1673166 c.-274C>T upstream_gene_variant 0.77 ethionamide
isoniazid
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 0.27 isoniazid Not assoc w R
katG 2156007 c.105C>T synonymous_variant 0.86 isoniazid Not assoc w R - Interim
PPE35 2168448 p.Gln722Arg missense_variant 0.72 pyrazinamide Uncertain significance
Rv1979c 2222852 p.Ala105Thr missense_variant 0.12 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223421 c.-257G>A upstream_gene_variant 0.74 clofazimine
bedaquiline
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449781 c.1278G>A synonymous_variant 0.23 ethionamide Not assoc w R - Interim
Rv3236c 3613354 c.-238G>T upstream_gene_variant 0.19 pyrazinamide
lpqB 3624486 p.Asp142Gly missense_variant 0.21 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627293 c.57G>A synonymous_variant 0.68 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.97 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.27 ethambutol Not assoc w R
aftB 4268477 c.360C>T synonymous_variant 0.21 ethambutol Not assoc w R - Interim
ubiA 4269351 c.483C>T synonymous_variant 0.16 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.17 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin