TB-Profiler result

Run: ERR4872093
Summary

Run ID: ERR4872093

Sample name:

Date: 2024-04-16T12:40:34.738110

Number of reads: 4642657

Percentage reads mapped: 89.69

Median coverage: 129.0

Strain: lineage5.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage5.2 West-Africa 1 RD711 1.0
lineage5 West-Africa 1 RD711 0.98
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Lys Assoc w R
p.His445Asp Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-29_-28delCT Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Gln10Pro Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fbiC c.859_861delATCinsGG Assoc w R - Interim Confers DLM-PMD cross-resistance
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
rpoB 761100 p.Gln432Lys missense_variant 0.93 rifampicin Assoc w R
rpoB 761139 p.His445Asp missense_variant 0.93 rifampicin Assoc w R
fbiC 1303789 c.859_861delATCinsGG frameshift_variant&missense_variant 0.14 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
katG 2155168 p.Ser315Thr missense_variant 0.93 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide Assoc w R
embA 4243203 c.-29_-28delCT upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.95 ethambutol 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
gyrB 6446 p.Ala403Ser missense_variant 0.97 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
gyrA 9566 c.2265C>T synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13579 c.-21G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 619519 c.-372C>T upstream_gene_variant 0.93 capreomycin
amikacin
kanamycin
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
Rv0565c 657649 c.-179G>A upstream_gene_variant 1.0 ethionamide
hadA 731750 c.-180G>C upstream_gene_variant 0.99 isoniazid
nusG 734457 c.204C>G synonymous_variant 0.14 rifampicin
nusG 734460 c.207G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
nusG 734472 c.219T>C synonymous_variant 0.16 rifampicin
nusG 734481 c.228C>T synonymous_variant 0.16 rifampicin
nusG 734532 c.279A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760841 c.1035T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760845 p.Thr347Ala missense_variant 0.14 rifampicin
rpoB 760859 c.1053T>C synonymous_variant 0.14 rifampicin
rpoB 760862 c.1056G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760925 c.1119T>C synonymous_variant 0.15 rifampicin
rpoB 760928 c.1122G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760934 c.1128C>T synonymous_variant 0.16 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760982 c.1176G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762131 c.2325C>G synonymous_variant 0.15 rifampicin
rpoB 762140 c.2334G>C synonymous_variant 0.14 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 0.14 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763702 c.333C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763774 c.405G>C synonymous_variant 0.14 rifampicin
rpoC 763792 p.Glu141Asp missense_variant 0.14 rifampicin
rpoC 766864 c.3495G>C synonymous_variant 0.13 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.15 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.15 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.16 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767011 c.3642G>C synonymous_variant 0.13 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 781715 c.156T>C synonymous_variant 0.15 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.15 streptomycin
rpsL 781736 c.177T>C synonymous_variant 0.14 streptomycin
rpsL 781742 c.183C>T synonymous_variant 0.14 streptomycin
rpsL 781748 c.189C>G synonymous_variant 0.16 streptomycin
rpsL 781754 c.195G>T synonymous_variant 0.16 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.17 streptomycin
rpsL 781772 c.213C>T synonymous_variant 0.15 streptomycin Not assoc w R - Interim
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
fbiC 1303761 c.831T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303785 c.855G>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303797 c.867A>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303818 c.888C>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303827 c.897A>G synonymous_variant 0.14 clofazimine
pretomanid
delamanid
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476723 n.3066T>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
fabG1 1673338 c.-102G>A upstream_gene_variant 1.0 ethionamide
isoniazid
rpsA 1834609 c.1068T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.15 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.15 pyrazinamide
tsnR 1853565 c.-41G>A upstream_gene_variant 1.0 linezolid Uncertain significance
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
ndh 2101921 c.1122G>A synonymous_variant 0.97 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ndh 2103112 c.-70G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290062 c.-821G>A upstream_gene_variant 0.97 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
Rv2477c 2783116 c.927T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783914 c.129T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3064664 p.Lys510Gln missense_variant 0.98 ethambutol Uncertain significance
moxifloxacin
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyX 3067949 c.-4C>T upstream_gene_variant 0.99 para-aminosalicylic_acid
thyA 3073920 c.552C>G synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073977 c.495A>G synonymous_variant 0.14 para-aminosalicylic_acid
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
ald 3087172 p.Glu118Ala missense_variant 0.99 cycloserine
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0 cycloserine
Rv3236c 3612237 p.Ala294Ser missense_variant 0.99 pyrazinamide
lpqB 3624350 c.561G>T synonymous_variant 1.0 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
alr 3840932 c.489C>T synonymous_variant 0.98 cycloserine
rpoA 3877679 p.Ala277Ser missense_variant 0.14 rifampicin
rpoA 3877692 c.816G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877743 c.765T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877791 c.717C>G synonymous_variant 0.14 rifampicin
ddn 3986987 c.144G>T synonymous_variant 1.0 delamanid Not assoc w R - Interim
pretomanid
ddn 3987180 p.Asp113Asn missense_variant 1.0 delamanid Uncertain significance
pretomanid
clpC1 4038755 c.1950G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040824 c.-120C>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 4139131 p.Glu209Lys missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 1.0 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244635 p.Val468Ala missense_variant 0.98 ethambutol Not assoc w R - Interim
embA 4245147 p.Pro639Ser missense_variant 0.92 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4249495 c.2982C>T synonymous_variant 0.94 ethambutol Not assoc w R - Interim
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
ethA 4326914 p.Ala187Glu missense_variant 1.0 ethionamide Uncertain significance
ethA 4327103 p.Gly124Asp missense_variant 1.0 ethionamide Uncertain significance
ethR 4328190 p.Glu214Asp missense_variant 1.0 ethionamide
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
gid 4407946 p.Leu86Pro missense_variant 1.0 streptomycin Uncertain significance