TB-Profiler result

Run: ERR4796743
Summary

Run ID: ERR4796743

Sample name:

Date: 2024-03-26T18:27:20.620942

Number of reads: 6431818

Percentage reads mapped: 99.58

Median coverage: 169.0

Strain: lineage1.2.2.2;lineage2.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.21
lineage2 East-Asian RD105 0.78
lineage1.2.2.2 Indo-Oceanic RD239 0.24
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.74
lineage2.2 East-Asian (Beijing) RD105;RD207 0.8
lineage1 Indo-Oceanic RD239 0.26
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Gly406Ser Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1390_1391dupGA Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.72 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.76 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.7 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 0.8 pyrazinamide Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.74 ethambutol Uncertain significance Mutation from literature
embB 4247729 p.Gly406Ser missense_variant 0.7 ethambutol Assoc w R
ethA 4326082 c.1390_1391dupGA frameshift_variant 0.81 ethionamide 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 5075 c.-165C>T upstream_gene_variant 0.24 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.28 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 0.31 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.14 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 13298 p.Ile87Met missense_variant 0.14 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.2 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.7 clofazimine Not assoc w R
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
mshA 575907 p.Ala187Val missense_variant 0.76 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.26 ethionamide
isoniazid
ccsA 620625 p.Ile245Met missense_variant 0.78 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.85 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.83 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.27 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.28 rifampicin Not assoc w R
nusG 734754 c.501G>C synonymous_variant 0.2 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.3 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.31 rifampicin Not assoc w R
rpoC 764666 p.Gly433Ser missense_variant 0.78 rifampicin Uncertain significance
rpoC 767011 c.3642G>C synonymous_variant 0.26 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
mmpL5 776182 p.Asp767Asn missense_variant 0.81 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 777598 c.883C>A synonymous_variant 0.17 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.28 linezolid Not assoc w R
Rv1129c 1253930 p.Phe202Tyr missense_variant 0.74 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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.14 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.14 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.24 ethambutol
rrs 1471506 n.-340G>A upstream_gene_variant 0.2 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474687 n.1030C>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.76 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.25 linezolid 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 0.24 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2064486 c.243A>G synonymous_variant 0.12 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.12 pyrazinamide Uncertain significance
Rv1979c 2221725 c.1440T>G synonymous_variant 0.18 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
Rv1979c 2222308 p.Asp286Gly missense_variant 0.15 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.22 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.18 isoniazid
eis 2714152 p.Val394Ala missense_variant 0.24 amikacin
kanamycin
ahpC 2726051 c.-142G>A upstream_gene_variant 0.25 isoniazid
Rv2752c 3064889 p.Lys435Glu missense_variant 0.2 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
thyA 3074422 p.Pro17Leu missense_variant 0.24 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.19 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.15 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.79 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627602 c.-253C>T upstream_gene_variant 0.16 bedaquiline Uncertain significance
rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.18 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.3 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
embC 4240671 p.Thr270Ile missense_variant 0.28 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.77 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.21 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.68 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.21 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.37 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.72 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.24 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.18 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.16 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 4338603 c.-82C>T upstream_gene_variant 0.23 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338635 c.-114A>C upstream_gene_variant 0.26 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 4407620 p.Tyr195His missense_variant 0.83 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.2 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.74 streptomycin Not assoc w R