TB-Profiler result

Run: ERR176631
Summary

Run ID: ERR176631

Sample name:

Date: 2025-09-15T14:01:43.936211

Number of reads: 3572273

Percentage reads mapped: 84.63

Median coverage: 81.0

Strain: lineage1.1.2;lineage4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1 Indo-Oceanic RD239 95.08
lineage1.1 Indo-Oceanic RD239 95.83
lineage1.1.2 Indo-Oceanic RD239 95.2
lineage4 Euro-American None 4.53
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
gyrB 6112 p.Met291Ile missense_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.96 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 0.92 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.92 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 0.94 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.93 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.94 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.96 ethionamide Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.93 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.96 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.94 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 0.99 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
rplC 800357 c.-452C>A upstream_gene_variant 0.9 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.95 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 0.92 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.94 ethambutol Uncertain significance
embR 1417793 c.-446C>T upstream_gene_variant 0.94 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
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.22 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.21 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.25 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.24 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.24 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.17 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.12 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.18 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.16 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.24 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.19 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476624 n.2967T>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673283 c.-919A>C upstream_gene_variant 0.91 ethionamide Uncertain significance
isoniazid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.93 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.91 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917777 c.-163A>G upstream_gene_variant 1.0 capreomycin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918106 p.Thr56Ile missense_variant 0.94 capreomycin Uncertain significance
bacA 2062922 p.Ile603Val missense_variant 0.99 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.98 isoniazid Not assoc w R
katG 2155557 c.555C>T synonymous_variant 0.96 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.92 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.92 pyrazinamide Uncertain significance
PPE35 2170378 p.Ala79Thr missense_variant 0.93 pyrazinamide Uncertain significance
Rv1979c 2221783 p.Ala461Glu missense_variant 0.97 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99 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 c.18C>T synonymous_variant 0.9 isoniazid Uncertain significance
eis 2714199 p.Lys378Asn missense_variant 0.91 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.94 isoniazid Uncertain significance
ahpC 2726672 c.480G>A synonymous_variant 0.97 isoniazid Not assoc w R - Interim
Rv2681 2996912 c.174C>T synonymous_variant 0.95 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448442 c.-62A>C upstream_gene_variant 0.95 ethionamide Uncertain significance
Rv3083 3448714 p.Asp71His missense_variant 0.97 ethionamide Uncertain significance
Rv3236c 3613012 c.105G>A synonymous_variant 0.94 pyrazinamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.91 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640253 c.-290T>C upstream_gene_variant 0.94 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.92 pyrazinamide Not assoc w R - Interim
panD 4044928 c.-647G>T upstream_gene_variant 0.96 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.99 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 4240671 p.Thr270Ile missense_variant 0.92 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.99 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 0.99 ethambutol Not assoc w R
embA 4245166 p.Pro645Gln missense_variant 0.97 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.96 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.89 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.91 ethambutol Not assoc w R
ubiA 4269411 c.423T>C synonymous_variant 0.11 ethambutol Not assoc w R - Interim
ubiA 4269606 c.228T>C synonymous_variant 0.96 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 0.97 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 0.95 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.93 streptomycin Not assoc w R