TB-Profiler result

Run: ERR3470647
Summary

Run ID: ERR3470647

Sample name:

Date: 2024-10-04T21:44:44.411014

Number of reads: 2238500

Percentage reads mapped: 91.14

Median coverage: 70.0

Strain: lineage3

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.99
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 rpsL p.Lys88Met Assoc w R
gid c.102delG Assoc w R
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
rpsL 781822 p.Lys88Met missense_variant 0.95 streptomycin Assoc w R
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin Assoc w R
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 6616 c.-686A>G upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 6622 c.-680C>T upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 6700 c.-602T>C upstream_gene_variant 0.13 levofloxacin
moxifloxacin
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
gyrA 9596 c.2295G>T synonymous_variant 0.93 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13277 c.282T>C synonymous_variant 1.0 isoniazid Not assoc w R
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
nusG 734354 p.Pro34Leu missense_variant 0.98 rifampicin Not assoc w R
nusG 734753 p.Thr167Met missense_variant 0.98 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 760223 c.417T>C synonymous_variant 0.14 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762246 c.2440C>T synonymous_variant 0.17 rifampicin
rpoB 762254 c.2448T>G synonymous_variant 0.14 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 762989 c.-381G>C upstream_gene_variant 0.15 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.19 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764112 p.Tyr248Phe missense_variant 0.14 rifampicin
rpoC 764116 c.747C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.14 rifampicin
rpoC 764140 c.771C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764181 p.Asp271Gly missense_variant 0.86 rifampicin Not assoc w R
rpoC 764188 c.819A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764236 c.867G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764248 c.879C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764257 c.888G>C synonymous_variant 0.15 rifampicin
rpoC 764272 c.903G>C synonymous_variant 0.14 rifampicin
rpoC 764353 c.984G>C synonymous_variant 0.13 rifampicin
rpoC 764434 c.1065A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764489 c.1120C>T synonymous_variant 0.13 rifampicin
rpoC 767033 c.3664_3666delTCGinsAGC synonymous_variant 0.15 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.15 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 767111 c.3742C>T synonymous_variant 0.16 rifampicin
rpoC 767119 c.3750A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.17 rifampicin
rpoC 767158 c.3789T>G synonymous_variant 0.15 rifampicin
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
fbiC 1304711 p.Ala594Asp missense_variant 0.12 pretomanid
delamanid
clofazimine
fbiC 1304742 c.1812T>C synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fbiC 1304757 c.1827A>G synonymous_variant 0.13 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472736 n.891G>A non_coding_transcript_exon_variant 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
inhA 1673985 c.-217C>G upstream_gene_variant 0.14 isoniazid
ethionamide
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 2063222 p.Pro503Ala missense_variant 0.99 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
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 2170769 c.-157C>T upstream_gene_variant 1.0 pyrazinamide
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
folC 2746810 p.Phe263Leu missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.97 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 2782990 c.1053C>G synonymous_variant 0.17 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
mtrA 3627119 c.231T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
rpoA 3878163 c.345C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878172 c.336G>C synonymous_variant 0.14 rifampicin
rpoA 3878226 c.282C>G synonymous_variant 0.17 rifampicin
rpoA 3878232 c.276G>C synonymous_variant 0.16 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.18 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.17 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.2 rifampicin
rpoA 3878310 c.198G>C synonymous_variant 0.21 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878334 c.174T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.25 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.27 rifampicin
rpoA 3878367 c.141C>G synonymous_variant 0.28 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.23 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.2 rifampicin
rpoA 3878388 c.120C>G synonymous_variant 0.2 rifampicin
rpoA 3878391 c.117T>C synonymous_variant 0.2 rifampicin
rpoA 3878415 c.93C>T synonymous_variant 0.18 rifampicin
rpoA 3878824 c.-317G>C upstream_gene_variant 0.15 rifampicin
rpoA 3878976 c.-469A>G upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoA 3878986 c.-479G>C upstream_gene_variant 0.21 rifampicin
rpoA 3878998 c.-491C>G upstream_gene_variant 0.2 rifampicin Uncertain significance
rpoA 3879022 c.-515G>C upstream_gene_variant 0.16 rifampicin
rpoA 3879079 c.-572A>G upstream_gene_variant 0.13 rifampicin
clpC1 4039121 c.1584T>C synonymous_variant 0.14 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
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