TB-Profiler result

Run: ERR403267
Summary

Run ID: ERR403267

Sample name:

Date: 2024-04-15T13:52:57.206661

Number of reads: 3978811

Percentage reads mapped: 99.62

Median coverage: 90.0

Strain: lineage2.2.1;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.27
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.24
lineage2.2 East-Asian (Beijing) RD105;RD207 0.25
lineage4 Euro-American None 0.73
lineage4.8 Euro-American (mainly T) RD219 0.72
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 embB p.Asp354Ala Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Cys72Arg Assoc w R
streptomycin rrs n.517C>T Assoc w R
gid c.628delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide ethA c.-7T>C Assoc w R - Interim
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
rpoB 761155 p.Ser450Leu missense_variant 0.26 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.25 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.23 isoniazid Assoc w R High-level resistance
pncA 2289028 p.Cys72Arg missense_variant 0.26 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 0.28 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embB 4247574 p.Asp354Ala missense_variant 0.25 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.75 ethambutol Assoc w R
ethA 4327480 c.-7T>C upstream_gene_variant 0.27 ethionamide Assoc w R - Interim
gid 4407574 c.628delC frameshift_variant 0.19 streptomycin 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 7196 p.Gly653Ser missense_variant 0.63 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.29 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.21 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.3 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.3 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.25 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.28 rifampicin Not assoc w R
rpoC 765462 p.Asn698Ser missense_variant 0.26 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.29 rifampicin Not assoc w R
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 0.25 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.2 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.27 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.31 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.35 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154503 p.Lys537Glu missense_variant 0.66 isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.29 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.22 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.75 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
ribD 2986827 c.-12G>A upstream_gene_variant 0.2 para-aminosalicylic_acid
ribD 2987532 p.Gly232Arg missense_variant 0.78 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.68 capreomycin
ald 3086705 c.-115T>G upstream_gene_variant 0.66 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.33 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.32 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.21 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038991 p.Gly572Ser missense_variant 0.63 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.32 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.26 ethambutol Not assoc w R
ubiA 4269864 c.-31C>T upstream_gene_variant 0.78 ethambutol Uncertain significance
whiB6 4338563 c.-42G>T upstream_gene_variant 0.21 capreomycin Not assoc w R
amikacin Uncertain significance
kanamycin 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 0.21 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.21 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.22 streptomycin Not assoc w R