TB-Profiler result

Run: ERR2515023
Summary

Run ID: ERR2515023

Sample name:

Date: 2025-05-15T23:46:23.546688

Number of reads: 6626754

Percentage reads mapped: 99.47

Median coverage: 217.0

Strain: lineage1.1.2;lineage4.4

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.37
lineage1.1 Indo-Oceanic RD239 0.37
lineage4 Euro-American None 0.64
lineage1 Indo-Oceanic RD239 0.36
lineage4.4 Euro-American None 0.47
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
dnaA 499 p.Ser167Arg missense_variant 0.5 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.39 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
Rv0010c 13298 p.Ile87Met missense_variant 0.38 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.29 isoniazid Not assoc w R
fgd1 491270 p.Tyr163Cys missense_variant 0.19 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.35 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.32 ethionamide Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.27 rifampicin Not assoc w R
rpoB 759546 c.-261A>G upstream_gene_variant 0.38 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.37 rifampicin Not assoc w R
rpoB 762368 non_coding_transcript_variant 0.56 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.41 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.4 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.4 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.35 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 0.41 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.35 bedaquiline Uncertain significance
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.35 linezolid Not assoc w R
Rv1129c 1253755 non_coding_transcript_variant 0.39 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.36 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.35 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.44 ethambutol Uncertain significance
embR 1417793 c.-446C>T upstream_gene_variant 0.35 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474571 n.914G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476121 n.2464C>A non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673280 c.-922C>T upstream_gene_variant 0.48 ethionamide Uncertain significance
isoniazid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.34 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.35 linezolid Not assoc w R
tsnR 1854241 c.636C>G synonymous_variant 0.17 linezolid Not assoc w R - Interim
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
bacA 2062922 p.Ile603Val missense_variant 0.32 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Not assoc w R
ndh 2101955 p.Gln363Ser missense_variant 0.34 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.38 isoniazid Not assoc w R
katG 2154915 c.1197A>G synonymous_variant 0.12 isoniazid Not assoc w R - Interim
PPE35 2167701 p.Ala971Gly missense_variant 0.36 pyrazinamide Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.33 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.31 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.39 bedaquiline Not assoc w R - Interim
clofazimine 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
kasA 2518132 non_coding_transcript_variant 0.37 isoniazid Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.37 isoniazid Uncertain significance
Rv2477c 2783201 p.Gln281Arg missense_variant 0.29 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2681 2996912 c.174C>T synonymous_variant 0.39 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.36 ethambutol Not assoc w R
isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv2752c 3066501 c.-310G>A upstream_gene_variant 0.15 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448714 p.Asp71His missense_variant 0.36 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.36 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.29 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
fbiA 3640308 c.-235C>T upstream_gene_variant 0.18 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.39 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.37 pyrazinamide Uncertain significance
panD 4044985 c.-704G>A upstream_gene_variant 0.41 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.41 ethambutol Not assoc w R
isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.53 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.39 ethambutol Not assoc w R
embC 4241005 non_coding_transcript_variant 0.38 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.38 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.4 ethambutol Not assoc w R
embA 4245218 c.1986C>T synonymous_variant 0.41 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.33 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.32 ethambutol Not assoc w R
aftB 4267118 c.1719G>A synonymous_variant 0.4 ethambutol Not assoc w R - Interim
ubiA 4268928 c.906C>T synonymous_variant 0.41 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.37 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.49 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.36 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.3 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.37 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.37 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.35 streptomycin Not assoc w R