TB-Profiler result

Run: ERR403282
Summary

Run ID: ERR403282

Sample name:

Date: 2024-10-04T12:51:28.620221

Number of reads: 3817087

Percentage reads mapped: 99.62

Median coverage: 88.0

Strain: lineage2.2.1;lineage4.3.3

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
lineage4.3 Euro-American (LAM) None 0.21
lineage2 East-Asian RD105 0.83
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.81
lineage2.2 East-Asian (Beijing) RD105;RD207 0.81
lineage4 Euro-American None 0.18
lineage4.3.3 Euro-American (LAM) RD115 0.19
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
p.Glu761Asp Uncertain significance Mutation from literature
rpoC p.Ile491Thr Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Asp354Ala Assoc w R
pyrazinamide pncA p.Trp119Arg Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
c.-37G>T Assoc w R
cycloserine
ethionamide ethA c.1010delT Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.47 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.88 rifampicin Assoc w R
rpoB 762089 p.Glu761Asp missense_variant 0.18 rifampicin Uncertain significance Mutation from literature
rpoC 764841 p.Ile491Thr missense_variant 0.57 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.19 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.79 isoniazid Assoc w R High-level resistance
pncA 2288887 p.Trp119Arg missense_variant 0.58 pyrazinamide Assoc w R - Interim
eis 2715342 c.-10G>A upstream_gene_variant 0.67 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
eis 2715369 c.-37G>T upstream_gene_variant 0.14 kanamycin Assoc w R
embB 4247429 p.Met306Val missense_variant 0.67 ethambutol Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.21 ethambutol Assoc w R
ethA 4326463 c.1010delT frameshift_variant 0.62 ethionamide Assoc w R
ethA 4327480 c.-7T>C upstream_gene_variant 0.15 ethionamide Assoc w R - Interim
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 8040 p.Gly247Ser missense_variant 0.13 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 13471 p.Leu30Val missense_variant 0.22 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.83 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.83 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.84 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.77 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.81 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.73 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.16 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.82 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.83 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.21 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
sigE 1364706 c.294G>A synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.74 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.85 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.19 pyrazinamide Not assoc w R - Interim
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 0.79 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.2 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.75 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289226 p.Ile6Leu missense_variant 0.13 pyrazinamide Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.17 isoniazid
ribD 2986827 c.-12G>A upstream_gene_variant 0.61 para-aminosalicylic_acid
Rv2752c 3064895 p.Ala433Ser missense_variant 0.56 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.17 para-aminosalicylic_acid
ald 3086731 c.-89A>G upstream_gene_variant 0.63 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.82 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.18 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.55 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.83 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.73 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.64 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338563 c.-42G>T upstream_gene_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.83 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.84 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.18 streptomycin Not assoc w R