TB-Profiler result

Run: ERR9787223
Summary

Run ID: ERR9787223

Sample name:

Date: 2024-04-15T14:26:53.383968

Number of reads: 3996827

Percentage reads mapped: 88.85

Median coverage: 194.0

Strain: lineage6.3.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage6.3 West-Africa 2 RD702 0.99
lineage6.3.1 West-Africa 2 RD702 0.99
lineage6 West-Africa 2 RD702 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
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 6446 p.Ala403Ser missense_variant 0.93 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
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 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
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 1.0 isoniazid Not assoc w R
fgd1 491668 p.Lys296Glu missense_variant 0.98 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 619628 c.-263G>A upstream_gene_variant 0.93 capreomycin
amikacin
kanamycin
ccsA 619862 c.-29G>A upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
Rv0565c 656432 p.Gly347Ser missense_variant 0.95 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734151 c.-103G>C upstream_gene_variant 0.99 rifampicin Uncertain significance
rpoB 760424 c.618C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760969 p.Ser388Leu missense_variant 0.94 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.91 rifampicin Not assoc w R
rpoB 762338 c.2532T>C synonymous_variant 0.14 rifampicin
rpoC 762410 c.-960T>C upstream_gene_variant 0.14 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.17 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.15 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.99 rifampicin Not assoc w R
rpoC 763675 c.306C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763774 c.405G>C synonymous_variant 0.14 rifampicin
rpoC 764554 c.1185C>T synonymous_variant 0.14 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764815 c.1446A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>T synonymous_variant 0.14 rifampicin
rpoC 765850 c.2481G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765892 c.2523T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766549 c.3180G>C synonymous_variant 0.15 rifampicin
rpoC 766573 c.3204T>C synonymous_variant 0.16 rifampicin
rpoC 766582 c.3213C>G synonymous_variant 0.14 rifampicin
rpoC 766583 c.3214_3216delGGTinsAC frameshift_variant&missense_variant 0.14 rifampicin
rpoC 766588 p.Glu1073Asp missense_variant 0.15 rifampicin Uncertain significance
rpoC 766594 c.3225G>C synonymous_variant 0.15 rifampicin
rpoC 766597 c.3228C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766607 p.Ile1080Leu missense_variant 0.16 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.16 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.18 rifampicin
rpoC 766660 c.3291G>C synonymous_variant 0.17 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.18 rifampicin
rpoC 766673 p.Gly1102Asn missense_variant 0.18 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.16 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.16 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 766876 c.3507C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766882 c.3513C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766900 c.3531T>C synonymous_variant 0.17 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.17 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.15 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.16 rifampicin
rpoC 767014 c.3645G>C synonymous_variant 0.17 rifampicin
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.18 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.16 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.15 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
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
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
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
atpE 1461251 c.207G>T synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
inhA 1674434 p.Val78Ala missense_variant 0.96 ethionamide Uncertain significance
isoniazid 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 2063121 c.1608A>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
ndh 2102694 p.Val117Ile missense_variant 0.98 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2222852 p.Ala105Thr missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
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
Rv2477c 2783040 p.Ala335Thr missense_variant 0.16 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2477c 2783044 c.999G>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783048 p.Asp332Gly missense_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783059 c.984T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783068 p.Asp325Glu missense_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783077 c.966T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783092 c.951A>G synonymous_variant 0.15 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2783095 c.948C>G synonymous_variant 0.14 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
amikacin Not assoc w R - Interim
Rv2477c 2783098 c.945C>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783101 c.942G>T synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783116 c.927T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783140 c.903C>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783146 c.897G>A synonymous_variant 0.15 ethambutol
moxifloxacin Not assoc w R - Interim
streptomycin
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin
amikacin Not assoc w R - Interim
Rv2477c 2783149 c.894G>C synonymous_variant 0.15 ethambutol
moxifloxacin Not assoc w R - Interim
streptomycin
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
thyX 3067490 c.456C>G synonymous_variant 0.15 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
Rv3083 3449781 c.1278G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3236c 3613354 c.-238G>T upstream_gene_variant 1.0 pyrazinamide
lpqB 3624350 c.561G>T synonymous_variant 0.96 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
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
mtrA 3627071 c.279G>T synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627098 c.252A>C synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627104 c.-491C>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrA 3627119 c.231T>G synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627122 c.-509T>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627167 c.-554T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
alr 3841377 p.Thr15Ile missense_variant 1.0 cycloserine
rpoA 3877679 p.Ala277Ser missense_variant 0.15 rifampicin
rpoA 3877696 p.Thr271Ile missense_variant 0.85 rifampicin Uncertain significance
rpoA 3877704 c.804G>C synonymous_variant 0.15 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878292 c.216T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.16 rifampicin
rpoA 3878310 c.198G>C synonymous_variant 0.16 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.16 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.15 rifampicin
rpoA 3878367 c.141C>G synonymous_variant 0.15 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.17 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.16 rifampicin
rpoA 3878388 c.120C>G synonymous_variant 0.16 rifampicin
rpoA 3878391 c.117T>C synonymous_variant 0.17 rifampicin
rpoA 3878415 c.93C>T synonymous_variant 0.18 rifampicin
rpoA 3878424 c.84G>C synonymous_variant 0.17 rifampicin
rpoA 3878436 c.72A>G synonymous_variant 0.16 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.16 rifampicin
rpoA 3878454 c.54A>C synonymous_variant 0.15 rifampicin
rpoA 3878785 c.-278T>G upstream_gene_variant 0.14 rifampicin
rpoA 3878788 c.-281G>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878806 c.-299C>G upstream_gene_variant 0.16 rifampicin
rpoA 3878809 c.-302T>C upstream_gene_variant 0.16 rifampicin
rpoA 3878818 c.-311G>A upstream_gene_variant 0.14 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.19 rifampicin Uncertain significance
rpoA 3878890 c.-383C>G upstream_gene_variant 0.2 rifampicin
rpoA 3878896 c.-389G>C upstream_gene_variant 0.2 rifampicin
rpoA 3878909 c.-402A>G upstream_gene_variant 0.19 rifampicin
rpoA 3878914 c.-407T>C upstream_gene_variant 0.19 rifampicin Uncertain significance
rpoA 3878917 c.-410G>A upstream_gene_variant 0.2 rifampicin Uncertain significance
rpoA 3878932 c.-425G>A upstream_gene_variant 0.21 rifampicin
rpoA 3878938 c.-431T>C upstream_gene_variant 0.22 rifampicin
rpoA 3878947 c.-440G>C upstream_gene_variant 0.21 rifampicin Uncertain significance
rpoA 3878968 c.-461T>C upstream_gene_variant 0.23 rifampicin Uncertain significance
rpoA 3878976 c.-469A>G upstream_gene_variant 0.22 rifampicin Uncertain significance
rpoA 3878986 c.-479G>C upstream_gene_variant 0.21 rifampicin
rpoA 3878998 c.-491C>G upstream_gene_variant 0.22 rifampicin Uncertain significance
rpoA 3879005 c.-499_-498delAAinsCG upstream_gene_variant 0.21 rifampicin
rpoA 3879013 c.-506A>G upstream_gene_variant 0.19 rifampicin
rpoA 3879079 c.-572A>G upstream_gene_variant 0.17 rifampicin
rpoA 3879088 c.-581A>C upstream_gene_variant 0.17 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.16 rifampicin
clpC1 4040926 c.-222C>T upstream_gene_variant 1.0 pyrazinamide
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
glpK 4139183 c.572dupG frameshift_variant 0.9 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.96 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.96 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
aftB 4268477 c.360C>T synonymous_variant 0.98 ethambutol Not assoc w R - Interim
ubiA 4268953 p.Thr294Met missense_variant 1.0 ethambutol
ubiA 4269351 c.483C>T synonymous_variant 0.91 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 1.0 ethionamide Uncertain significance
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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R