TB-Profiler result

Run: SRR7070041
Summary

Run ID: SRR7070041

Sample name:

Date: 2024-10-04T19:45:27.512451

Number of reads: 1974590

Percentage reads mapped: 90.1

Median coverage: 58.0

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
mshA 575821 c.474G>C synonymous_variant 0.14 isoniazid
ethionamide
rpoB 760298 c.492G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760331 c.525G>C synonymous_variant 0.13 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761213 c.1407G>C synonymous_variant 0.14 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.12 rifampicin
rpoB 763136 c.3330C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763190 c.-180C>T upstream_gene_variant 0.12 rifampicin
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
fbiC 1304829 c.1899T>C synonymous_variant 0.15 pretomanid
delamanid
clofazimine
fbiC 1304832 c.1902C>T synonymous_variant 0.16 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304862 c.1932G>A synonymous_variant 0.21 pretomanid
delamanid
clofazimine
fbiC 1304869 c.1939C>T synonymous_variant 0.21 pretomanid
delamanid
clofazimine
fbiC 1304875 p.Ile649Val missense_variant 0.21 pretomanid
delamanid
clofazimine
fbiC 1304883 p.Glu651Asp missense_variant 0.21 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833940 c.399C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833971 c.430C>T synonymous_variant 0.16 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
Rv2680 2995860 c.-245C>T upstream_gene_variant 1.0 capreomycin
whiB7 3568610 p.Asp24His missense_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
lpqB 3624050 c.861C>G synonymous_variant 0.12 rifampicin
bedaquiline
lpqB 3624077 c.834G>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3624082 c.829A>C synonymous_variant 0.12 rifampicin
bedaquiline
alr 3840618 p.Asp268Gly missense_variant 1.0 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243929 p.Leu233Met missense_variant 1.0 ethambutol Uncertain significance
embB 4247535 p.Thr341Asn missense_variant 0.98 ethambutol Uncertain significance
embB 4249732 c.3219C>G synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267604 c.1233C>G synonymous_variant 0.13 ethambutol
aftB 4267607 c.1230G>A synonymous_variant 0.14 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R