TB-Profiler result

Run: SRR29126968
Summary

Run ID: SRR29126968

Sample name:

Date: 2025-02-11T10:44:10.135805

Number of reads: 2037850

Percentage reads mapped: 97.57

Median coverage: 50.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.7 Euro-American (mainly T) None 1.0
lineage4 Euro-American None 1.0
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
hadA 731732 c.-198G>A upstream_gene_variant 0.13 isoniazid
hadA 731747 c.-183T>C upstream_gene_variant 0.12 isoniazid
rpoB 760406 c.600G>C synonymous_variant 0.15 rifampicin
rpoB 760412 c.606C>G synonymous_variant 0.15 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 761207 c.1401C>T synonymous_variant 0.14 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.14 rifampicin
rpoB 761219 c.1413G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762246 c.2440C>T synonymous_variant 0.15 rifampicin
rpoB 762254 c.2448T>G synonymous_variant 0.16 rifampicin
rpoB 762257 c.2451C>G synonymous_variant 0.14 rifampicin
rpoB 762266 c.2460T>C synonymous_variant 0.13 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762317 c.2511A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.16 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.16 rifampicin
rpoB 762369 c.2563T>C synonymous_variant 0.14 rifampicin
rpoB 762404 c.2598T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 762410 c.-960T>C upstream_gene_variant 0.17 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 762419 c.-951C>G upstream_gene_variant 0.16 rifampicin
rpoC 762434 c.-936T>C upstream_gene_variant 0.17 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762995 c.3189G>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.24 rifampicin
rpoC 763025 c.-345C>T upstream_gene_variant 0.21 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.17 rifampicin
rpoC 765751 c.2382C>G synonymous_variant 0.17 rifampicin
rpoC 765753 p.Asp795Ala missense_variant 0.15 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781700 c.141G>C synonymous_variant 0.12 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.12 streptomycin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833721 c.180A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833748 c.207C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.23 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.21 pyrazinamide
rpsA 1833971 c.430C>T synonymous_variant 0.21 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.2 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.19 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168370 p.Ala748Glu missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2517950 c.-165C>G upstream_gene_variant 0.14 isoniazid
Rv2477c 2783593 c.450T>C synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783605 c.438T>C synonymous_variant 0.18 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783620 c.423C>G synonymous_variant 0.26 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783628 p.Ala139Ser missense_variant 0.29 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783656 c.387G>C synonymous_variant 0.3 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.3 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783674 c.369T>C synonymous_variant 0.28 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.24 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.23 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783718 c.325T>C synonymous_variant 0.2 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783719 c.324A>G synonymous_variant 0.21 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783751 p.Ile98Val missense_variant 0.21 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
mtrB 3626687 c.-74G>T upstream_gene_variant 0.13 rifampicin
bedaquiline
rpoA 3878938 c.-431T>A upstream_gene_variant 0.15 rifampicin
rpoA 3878947 c.-440G>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878962 c.-455G>A upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoA 3878968 c.-461T>C upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoA 3878976 c.-469A>G upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878986 c.-479G>C upstream_gene_variant 0.14 rifampicin
clpC1 4038845 c.1860G>C synonymous_variant 0.19 pyrazinamide
clpC1 4038860 c.1845G>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038914 c.1791G>C synonymous_variant 0.11 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_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