TB-Profiler result

Run: SRR29096943
Summary

Run ID: SRR29096943

Sample name:

Date: 2025-02-11T11:27:06.945511

Number of reads: 608164

Percentage reads mapped: 95.56

Median coverage: 19.0

Strain: lineage3.1.2.1

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
lineage3.1.2 East-African-Indian RD750 0.96
lineage3.1.2.1 East-African-Indian RD750 0.98
lineage3.1 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 8339 c.1038A>C synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 8340 p.Ala347Ser missense_variant 0.33 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8375 c.1074G>C synonymous_variant 0.36 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 8382 p.Leu361Met missense_variant 0.38 levofloxacin
moxifloxacin
gyrA 8391 p.Tyr364His missense_variant 0.35 levofloxacin
moxifloxacin
gyrA 8399 c.1098T>C synonymous_variant 0.35 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8401 p.Asp367Ala missense_variant 0.39 levofloxacin
moxifloxacin
gyrA 8408 c.1107A>G synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrA 8417 c.1116C>G synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 8420 c.1119T>C synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 8438 c.1137C>T synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 8453 c.1152A>C synonymous_variant 0.3 levofloxacin
moxifloxacin
gyrA 8462 c.1161A>G synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491595 c.813C>G synonymous_variant 0.44 pretomanid
delamanid
clofazimine
fgd1 491601 c.819T>C synonymous_variant 0.44 pretomanid
delamanid
clofazimine
fgd1 491610 c.828A>G synonymous_variant 0.44 pretomanid
delamanid
clofazimine
fgd1 491616 c.834A>G synonymous_variant 0.48 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
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
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 763714 c.345G>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764134 c.765C>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764188 c.819A>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 764203 c.834G>C synonymous_variant 0.47 rifampicin
rpoC 764206 c.837T>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 764207 p.Val280Thr missense_variant 0.5 rifampicin Uncertain significance
rpoC 764213 p.Arg282Lys missense_variant 0.52 rifampicin Uncertain significance
rpoC 764242 c.873C>T synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoC 764257 c.888G>C synonymous_variant 0.48 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 764287 c.918C>T synonymous_variant 0.45 rifampicin
rpoC 764293 c.924G>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 764311 c.942C>G synonymous_variant 0.38 rifampicin
rpoC 764489 c.1120C>T synonymous_variant 0.5 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 764503 c.1134G>C synonymous_variant 0.58 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.61 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>C synonymous_variant 0.66 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.72 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.6 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>T synonymous_variant 0.57 rifampicin
rpoC 764887 c.1518G>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 764908 c.1539G>A synonymous_variant 0.52 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.52 rifampicin
rpoC 764912 p.Met515Gln missense_variant 0.52 rifampicin Uncertain significance
rpoC 764923 c.1554A>G synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764983 c.1614T>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.48 rifampicin Not assoc w R
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 1253278 c.1257C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834432 c.891G>T synonymous_variant 0.37 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.35 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.35 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.44 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.41 pyrazinamide
rpsA 1834732 c.1191T>C synonymous_variant 0.43 pyrazinamide
rpsA 1834738 c.1197A>G synonymous_variant 0.43 pyrazinamide
rpsA 1834747 c.1206A>G synonymous_variant 0.47 pyrazinamide
rpsA 1834751 p.Leu404Ile missense_variant 0.47 pyrazinamide
rpsA 1834756 c.1215G>A synonymous_variant 0.47 pyrazinamide
rpsA 1834759 c.1218A>T synonymous_variant 0.47 pyrazinamide
rpsA 1834765 p.Glu408Asp missense_variant 0.5 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
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
kasA 2517926 c.-189G>A upstream_gene_variant 0.24 isoniazid
eis 2714401 p.Ala311Val missense_variant 1.0 kanamycin
amikacin
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
ahpC 2726201 c.9G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
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 2783344 c.699C>G synonymous_variant 0.36 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783347 c.696C>G synonymous_variant 0.36 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783350 c.693T>C synonymous_variant 0.33 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783353 c.690T>C synonymous_variant 0.36 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783373 p.Glu224Gln missense_variant 0.39 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783395 c.648T>C synonymous_variant 0.33 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783422 c.621T>C synonymous_variant 0.35 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624132 p.Arg260Lys missense_variant 1.0 rifampicin Uncertain significance
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877647 c.861C>T synonymous_variant 0.44 rifampicin
rpoA 3877656 c.852T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.53 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoA 3877689 c.819C>G synonymous_variant 0.5 rifampicin
rpoA 3877692 c.816G>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoA 3877695 c.813C>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>T synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoA 3877737 c.771G>C synonymous_variant 0.42 rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
clpC1 4039286 c.1419T>G synonymous_variant 0.41 pyrazinamide
clpC1 4039292 c.1413C>T synonymous_variant 0.35 pyrazinamide
clpC1 4039295 c.1410A>T synonymous_variant 0.4 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.45 pyrazinamide
clpC1 4039313 c.1392C>T synonymous_variant 0.48 pyrazinamide
clpC1 4039319 c.1386T>C synonymous_variant 0.5 pyrazinamide Not assoc w R - Interim
clpC1 4039328 c.1377A>G synonymous_variant 0.48 pyrazinamide
clpC1 4039334 c.1371G>C synonymous_variant 0.48 pyrazinamide
clpC1 4039338 p.Thr456Gln missense_variant 0.48 pyrazinamide
clpC1 4039382 c.1323C>G synonymous_variant 0.47 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.42 pyrazinamide
clpC1 4039394 c.1311G>C synonymous_variant 0.42 pyrazinamide
clpC1 4039397 c.1308A>G synonymous_variant 0.41 pyrazinamide
clpC1 4039406 c.1299G>C synonymous_variant 0.35 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.35 pyrazinamide
clpC1 4039412 c.1293T>C synonymous_variant 0.35 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.35 pyrazinamide Uncertain significance
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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407568 p.Ala212Val missense_variant 0.92 streptomycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407855 c.348G>C synonymous_variant 0.94 streptomycin