TB-Profiler result

Run: ERR11465597
Summary

Run ID: ERR11465597

Sample name:

Date: 2024-04-16T11:41:17.174794

Number of reads: 3230213

Percentage reads mapped: 99.18

Median coverage: 85.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.99
lineage4.1.2 Euro-American None 0.98
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620367 c.477T>C synonymous_variant 0.13 capreomycin
amikacin
kanamycin
ccsA 620370 c.480C>T synonymous_variant 0.13 capreomycin
amikacin
kanamycin
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
hadA 731774 c.-156T>C upstream_gene_variant 0.18 isoniazid
hadA 731777 c.-153C>T upstream_gene_variant 0.17 isoniazid
hadA 731789 c.-141A>G upstream_gene_variant 0.15 isoniazid
hadA 731816 c.-114G>C upstream_gene_variant 0.11 isoniazid
rpoB 760115 c.309C>T synonymous_variant 0.95 rifampicin Not assoc w R
rpoB 761243 c.1437G>C synonymous_variant 0.12 rifampicin
rpoC 764044 c.675T>C synonymous_variant 0.14 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764194 p.Glu275Asp missense_variant 0.22 rifampicin
rpoC 764200 c.831G>T synonymous_variant 0.21 rifampicin
rpoC 764203 c.834G>T synonymous_variant 0.2 rifampicin
rpoC 764206 p.Asp279Glu missense_variant 0.21 rifampicin
rpoC 764209 c.840C>G synonymous_variant 0.21 rifampicin
rpoC 764215 c.846A>G synonymous_variant 0.21 rifampicin
rpoC 764242 c.873C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>G synonymous_variant 0.12 rifampicin
rpoC 764536 c.1167G>C synonymous_variant 0.14 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 0.99 rifampicin Not assoc w R
rpoC 766594 c.3225G>C synonymous_variant 0.16 rifampicin
rpoC 766607 c.3238_3240delATCinsCG frameshift_variant&missense_variant 0.16 rifampicin
rpoC 766645 c.3276A>G synonymous_variant 0.14 rifampicin
rpoC 766651 c.3282T>C synonymous_variant 0.13 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.12 rifampicin
rpoC 766774 c.3405T>C synonymous_variant 0.14 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766813 c.3444G>C synonymous_variant 0.15 rifampicin
rpoC 766861 c.3492G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.16 rifampicin
rpoC 766918 c.3549C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766933 c.3564A>G synonymous_variant 0.16 rifampicin
rpoC 766942 c.3573C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766945 c.3576A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766960 c.3591C>T synonymous_variant 0.24 rifampicin
rpoC 766963 c.3594T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.21 rifampicin
rpoC 766978 c.3609C>T synonymous_variant 0.2 rifampicin
rpoC 766981 c.3612T>C synonymous_variant 0.2 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 767002 c.3633G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767035 c.3666G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 767059 c.3690T>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.16 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.14 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 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 801152 p.Thr115Met missense_variant 1.0 linezolid
fbiC 1303520 p.Ser197Thr missense_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303590 c.660A>G synonymous_variant 0.12 clofazimine
pretomanid
delamanid
sigE 1364763 c.351T>C synonymous_variant 0.13 pyrazinamide
sigE 1364767 c.355A>C synonymous_variant 0.12 pyrazinamide
sigE 1364790 c.378T>C synonymous_variant 0.17 pyrazinamide
sigE 1364799 c.387G>C synonymous_variant 0.18 pyrazinamide
sigE 1364805 c.393C>G synonymous_variant 0.16 pyrazinamide
sigE 1364811 c.399A>G synonymous_variant 0.17 pyrazinamide
sigE 1364814 c.402C>T synonymous_variant 0.17 pyrazinamide
sigE 1364820 c.408A>G synonymous_variant 0.18 pyrazinamide
sigE 1364868 c.456T>C synonymous_variant 0.12 pyrazinamide
Rv1258c 1407079 c.261delC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.13 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474716 n.1059A>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474994 n.1337T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475603 n.1946G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475758 n.2104delC non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
inhA 1673946 c.-256C>G upstream_gene_variant 0.12 ethionamide
isoniazid
fabG1 1673960 p.Ala174Val missense_variant 0.16 ethionamide
isoniazid
inhA 1673976 c.-226T>C upstream_gene_variant 0.17 ethionamide
isoniazid
inhA 1673991 c.-211C>T upstream_gene_variant 0.18 ethionamide
isoniazid
inhA 1674006 c.-196T>C upstream_gene_variant 0.13 ethionamide
isoniazid
inhA 1674051 c.-151A>G upstream_gene_variant 0.15 ethionamide
isoniazid
inhA 1674054 c.-148T>C upstream_gene_variant 0.15 ethionamide
isoniazid
inhA 1674060 c.-142A>G upstream_gene_variant 0.22 ethionamide
isoniazid
fabG1 1674079 p.Pro214Ala missense_variant 0.17 ethionamide
isoniazid
inhA 1674084 c.-118C>T upstream_gene_variant 0.2 ethionamide
isoniazid
inhA 1674105 c.-97C>T upstream_gene_variant 0.2 ethionamide
isoniazid
inhA 1674129 c.-73C>T upstream_gene_variant 0.15 ethionamide
isoniazid
inhA 1674132 c.-70T>C upstream_gene_variant 0.15 ethionamide
isoniazid
inhA 1674141 c.-61T>C upstream_gene_variant 0.14 ethionamide
isoniazid
inhA 1674171 c.-31T>C upstream_gene_variant 0.16 ethionamide
isoniazid
inhA 1674199 c.-3C>G upstream_gene_variant 0.12 ethionamide
isoniazid Uncertain significance
inhA 1674345 c.144G>A synonymous_variant 0.13 ethionamide
isoniazid
rpsA 1833667 c.126C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833679 c.138G>T synonymous_variant 0.19 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.2 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.19 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833778 c.237C>T synonymous_variant 0.13 pyrazinamide
rpsA 1833781 c.240T>G synonymous_variant 0.12 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833916 c.375C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.17 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1834360 c.819G>A synonymous_variant 0.15 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834654 p.Glu371Asp missense_variant 0.12 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
PPE35 2169902 c.711G>C synonymous_variant 0.12 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
kasA 2518684 c.570C>G synonymous_variant 0.12 isoniazid
Rv2477c 2783656 c.387G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.16 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.14 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.19 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625510 c.-600T>G upstream_gene_variant 0.13 bedaquiline
rifampicin
lpqB 3625513 c.-603G>C upstream_gene_variant 0.13 bedaquiline
rifampicin
lpqB 3625518 c.-608T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
lpqB 3625522 c.-612C>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626885 c.-272A>C upstream_gene_variant 0.11 bedaquiline
rifampicin
mtrB 3626890 c.-277T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrB 3626996 c.-383G>C upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrB 3627008 c.-395G>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627011 c.-398T>G upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3627125 c.-512C>G upstream_gene_variant 0.14 bedaquiline
rifampicin
rpoA 3877613 p.Ile299Val missense_variant 0.19 rifampicin
rpoA 3877617 c.891G>C synonymous_variant 0.19 rifampicin
rpoA 3877638 c.870T>G synonymous_variant 0.12 rifampicin
rpoA 3877770 c.738A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877794 c.714G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877818 c.690A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3879121 c.-614T>G upstream_gene_variant 0.16 rifampicin
rpoA 3879127 c.-620T>C upstream_gene_variant 0.14 rifampicin
rpoA 3879145 c.-638G>C upstream_gene_variant 0.15 rifampicin
rpoA 3879160 c.-653A>G upstream_gene_variant 0.16 rifampicin
rpoA 3879175 c.-668C>G upstream_gene_variant 0.14 rifampicin
rpoA 3879178 c.-671T>C upstream_gene_variant 0.14 rifampicin
rpoA 3879194 c.-688_-687delCAinsGC upstream_gene_variant 0.11 rifampicin
clpC1 4038932 c.1773G>C synonymous_variant 0.13 pyrazinamide
clpC1 4040105 c.600C>G synonymous_variant 0.13 pyrazinamide
clpC1 4040644 c.61A>C synonymous_variant 0.14 pyrazinamide
clpC1 4040693 c.12A>T synonymous_variant 0.13 pyrazinamide
clpC1 4040699 c.6C>T synonymous_variant 0.16 pyrazinamide
glpK 4138696 p.Pro354Ala missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138706 c.1050C>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138712 c.1044G>T synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138721 c.1035G>A synonymous_variant 0.14 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138724 c.1032A>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138727 c.1029C>T synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138733 c.1023C>T synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138757 c.999A>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4239023 c.-840C>G upstream_gene_variant 0.12 ethambutol
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408123 p.Ala27Val missense_variant 1.0 streptomycin Uncertain significance