TB-Profiler result

Run: ERR176630
Summary

Run ID: ERR176630

Sample name:

Date: 2024-04-15T18:20:47.183683

Number of reads: 2497848

Percentage reads mapped: 95.47

Median coverage: 57.0

Strain: lineage1.1.3.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 1.0
lineage1.1.3.2 Indo-Oceanic RD239 1.0
lineage1.1 Indo-Oceanic RD239 1.0
lineage1 Indo-Oceanic RD239 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 rrs n.888G>A Uncertain significance Mutation from literature
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance Mutation from literature
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 1.0 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 8188 p.Leu296Pro missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_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
gyrA 9445 p.Asn715Ser missense_variant 0.97 levofloxacin
moxifloxacin
Rv0010c 13298 p.Ile87Met missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 619619 c.-272C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin
ccsA 619695 c.-196G>A upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.99 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.98 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.97 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid Not assoc w R
rplC 801166 p.Gly120Ser missense_variant 1.0 linezolid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.98 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.98 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674883 p.Ile228Val missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 1.0 linezolid Not assoc w R
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 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2064420 c.309C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
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
PPE35 2167983 p.Gly877Asp missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99 isoniazid
folC 2746207 c.1392C>T synonymous_variant 1.0 para-aminosalicylic_acid
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv2752c 3065448 c.744C>T synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642173 c.639G>A synonymous_variant 1.0 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4238874 c.-989A>C upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.98 ethambutol Not assoc w R
embA 4242418 c.-815C>A upstream_gene_variant 1.0 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338568 c.-47G>A upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 1.0 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R