TB-Profiler result

Run: SRR29603691
Summary

Run ID: SRR29603691

Sample name:

Date: 2025-02-11T19:39:48.409745

Number of reads: 2278234

Percentage reads mapped: 97.98

Median coverage: 76.0

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 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
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 490679 c.-103_-98delAGCCGG upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
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
mmaA3 737384 p.Ala256Ser missense_variant 1.0 isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 761027 c.1221A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763732 c.363C>G synonymous_variant 0.12 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.12 rifampicin
rpoC 763835 p.Ala156Met missense_variant 0.12 rifampicin
rpoC 764112 p.Tyr248Phe missense_variant 0.12 rifampicin
rpoC 764236 c.867G>A synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>A synonymous_variant 0.12 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.11 rifampicin
rpoC 766861 c.3492G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.15 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.2 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.16 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
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
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 1406804 c.537G>A synonymous_variant 1.0 streptomycin
pyrazinamide
isoniazid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1475008 n.1351C>A non_coding_transcript_exon_variant 0.96 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
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
ndh 2103221 c.-179C>T upstream_gene_variant 1.0 isoniazid
delamanid
ethionamide
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
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2477c 2783839 c.204C>G synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783843 p.Gly67Asp missense_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783846 p.Thr66Asn missense_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877782 c.726T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877791 c.717C>G synonymous_variant 0.15 rifampicin
rpoA 3877818 c.690A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.17 rifampicin
rpoA 3877866 c.642G>C synonymous_variant 0.19 rifampicin
rpoA 3877875 c.633T>G synonymous_variant 0.2 rifampicin
rpoA 3877878 c.630G>C synonymous_variant 0.19 rifampicin
rpoA 3877890 c.618C>T synonymous_variant 0.16 rifampicin
rpoA 3877900 p.Ser203Asn missense_variant 0.16 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877909 p.Asn200Ser missense_variant 0.15 rifampicin
rpoA 3877920 c.588G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877962 c.546G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877986 c.522G>C synonymous_variant 0.13 rifampicin
rpoA 3877989 c.519A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878001 c.507A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878022 c.486T>C synonymous_variant 0.13 rifampicin
rpoA 3878028 c.480G>C synonymous_variant 0.13 rifampicin
rpoA 3878031 c.477T>C synonymous_variant 0.13 rifampicin
rpoA 3878040 c.468T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878043 c.465G>A synonymous_variant 0.14 rifampicin
rpoA 3878055 c.453A>G synonymous_variant 0.13 rifampicin
rpoA 3878058 c.450G>T synonymous_variant 0.12 rifampicin
rpoA 3878061 c.447G>C synonymous_variant 0.12 rifampicin
rpoA 3878067 c.441C>G synonymous_variant 0.12 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3878271 c.237T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
clpC1 4038293 c.2412G>C synonymous_variant 0.12 pyrazinamide
clpC1 4038302 c.2403C>G synonymous_variant 0.12 pyrazinamide
clpC1 4038368 c.2337T>C synonymous_variant 0.12 pyrazinamide
clpC1 4038640 p.Asp689Asn missense_variant 0.12 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.13 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTTG synonymous_variant 0.13 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039004 c.1701C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.15 pyrazinamide
clpC1 4039064 c.1641C>T synonymous_variant 0.15 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040369 c.336C>G synonymous_variant 0.12 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4268117 c.720G>C synonymous_variant 0.18 ethambutol
aftB 4268123 p.Ser238Gly missense_variant 0.17 ethambutol
aftB 4268129 c.708T>G synonymous_variant 0.17 ethambutol
aftB 4268138 c.699A>C synonymous_variant 0.2 ethambutol Not assoc w R - Interim
aftB 4268144 c.693T>C synonymous_variant 0.18 ethambutol
aftB 4268164 p.Gln225Glu missense_variant 0.17 ethambutol
aftB 4268169 p.Ala223Gly missense_variant 0.18 ethambutol
aftB 4268171 c.666G>C synonymous_variant 0.18 ethambutol
aftB 4268179 c.658T>C synonymous_variant 0.18 ethambutol Not assoc w R - Interim
aftB 4268182 p.Phe219Leu missense_variant 0.18 ethambutol
aftB 4268183 c.654A>T synonymous_variant 0.18 ethambutol
aftB 4268193 p.Leu215Ala missense_variant 0.19 ethambutol
aftB 4268205 p.Val211Ala missense_variant 0.2 ethambutol
aftB 4268213 c.624T>G synonymous_variant 0.2 ethambutol
aftB 4268225 c.612G>C synonymous_variant 0.13 ethambutol
ethA 4326795 p.Arg227Cys missense_variant 1.0 ethionamide
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