TB-Profiler result

Run: ERR11081864
Summary

Run ID: ERR11081864

Sample name:

Date: 2024-04-15T10:53:20.017160

Number of reads: 5867255

Percentage reads mapped: 95.62

Median coverage: 180.0

Strain: lineage3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 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.462C>T 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 1472307 n.462C>T non_coding_transcript_exon_variant 0.14 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
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 1.0 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 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576108 p.Ala254Gly missense_variant 0.32 ethionamide
isoniazid
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
hadA 732396 p.Gly156Ala missense_variant 0.13 isoniazid
hadA 732398 p.Ala157Thr missense_variant 0.13 isoniazid
nusG 734354 p.Pro34Leu missense_variant 0.99 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 759875 c.69T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761306 c.1500C>G synonymous_variant 0.11 rifampicin
rpoB 762206 c.2400C>G synonymous_variant 0.12 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.99 rifampicin Not assoc w R
rpoB 762926 c.3120C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.13 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.15 rifampicin
rpoC 763025 c.-345C>T upstream_gene_variant 0.13 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.14 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 0.13 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.14 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.13 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.14 rifampicin
rpoC 764181 p.Asp271Gly missense_variant 0.91 rifampicin Not assoc w R
rpoC 764611 c.1242G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.15 rifampicin
rpoC 764932 c.1563C>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 0.14 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765019 c.1650A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765034 c.1665T>C synonymous_variant 0.16 rifampicin
rpoC 765040 c.1671T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765041 c.1672T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765047 c.1678T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765053 c.1684_1685delTCinsAG synonymous_variant 0.13 rifampicin
rpoC 765073 c.1704G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765076 c.1707A>G synonymous_variant 0.12 rifampicin
rpoC 765079 c.1710T>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765082 c.1713G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765625 c.2256C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765811 c.2442T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765814 c.2445A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765826 c.2457T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765850 c.2481G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
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 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
rpsL 781841 c.282C>G synonymous_variant 0.12 streptomycin
rplC 800693 c.-116A>G upstream_gene_variant 0.15 linezolid
rplC 800703 c.-106T>C upstream_gene_variant 0.15 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.16 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.16 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.17 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.15 linezolid
rplC 800771 c.-38C>T upstream_gene_variant 0.14 linezolid
Rv1129c 1254039 p.Asn166Asp missense_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rpsA 1833661 c.120A>G synonymous_variant 0.16 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833721 c.180A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.12 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.14 pyrazinamide
rpsA 1833748 c.207C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.13 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.13 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.13 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
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
kasA 2517950 c.-165C>G upstream_gene_variant 0.12 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.99 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2783605 c.438T>C synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783751 p.Ile98Val missense_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783758 p.Asp95Glu missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783761 c.282G>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783766 p.Met93Leu missense_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783776 c.267G>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783779 c.264T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783797 p.Asp82Glu missense_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783815 c.228A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783821 p.Gln74Leu missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783833 c.210G>C synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783839 c.204C>G synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783843 p.Gly67Asp missense_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783846 p.Thr66Asn missense_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783860 c.183T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783863 c.180C>T synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783883 c.160T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783884 c.159T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783887 c.156C>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783914 c.129T>C synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.24 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783929 c.114C>G synonymous_variant 0.31 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3065678 p.Lys172Glu missense_variant 0.99 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
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
mtrB 3627181 c.-568T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrB 3627182 c.-569T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrA 3627188 c.162A>G synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627209 c.-596G>A upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrA 3627221 c.129C>T synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627227 c.123T>C synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627233 c.-620T>C upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3627236 c.-623T>C upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrA 3627242 c.108C>T synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627254 c.-641C>T upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3627263 c.-650C>T upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627266 c.-653A>G upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627272 c.-659G>T upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627275 c.-662G>T upstream_gene_variant 0.15 bedaquiline
rifampicin
rpoA 3877743 c.765T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877791 c.717C>G synonymous_variant 0.13 rifampicin
rpoA 3877818 c.690A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877866 c.642G>C synonymous_variant 0.13 rifampicin
rpoA 3877986 c.522G>C synonymous_variant 0.12 rifampicin
rpoA 3878001 c.507A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878022 c.486T>C synonymous_variant 0.13 rifampicin
rpoA 3878028 c.480G>C synonymous_variant 0.12 rifampicin
rpoA 3878031 c.477T>C synonymous_variant 0.12 rifampicin
rpoA 3878106 c.402G>C synonymous_variant 0.12 rifampicin
rpoA 3878118 c.390T>C synonymous_variant 0.12 rifampicin
rpoA 3878346 c.162T>C synonymous_variant 0.13 rifampicin
rpoA 3878364 c.144A>T synonymous_variant 0.13 rifampicin
rpoA 3878367 c.141C>G synonymous_variant 0.13 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.13 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.13 rifampicin
rpoA 3878388 c.120C>G synonymous_variant 0.13 rifampicin
rpoA 3878391 c.117T>C synonymous_variant 0.13 rifampicin
clpC1 4039004 c.1701C>G synonymous_variant 0.12 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid 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 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
whiB6 4338794 c.-273A>G upstream_gene_variant 0.12 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4408002 p.Asp67Glu missense_variant 1.0 streptomycin Uncertain significance