TB-Profiler result

Run: ERR403299
Summary

Run ID: ERR403299

Sample name:

Date: 2024-10-04T05:17:08.707698

Number of reads: 6979089

Percentage reads mapped: 99.48

Median coverage: 158.0

Strain: lineage2.2.1;lineage4.2.1.1;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.1
lineage4.2 Euro-American None 0.57
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.1
lineage2.2 East-Asian (Beijing) RD105;RD207 0.09
lineage4 Euro-American None 0.89
lineage4.2.1.1 Euro-American (TUR) None 0.56
lineage4.8 Euro-American (mainly T) RD219 0.34
lineage4.2.1 Euro-American (TUR) None 0.53
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-37G>T Assoc w R
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
katG 2155168 p.Ser315Thr missense_variant 0.67 isoniazid Assoc w R High-level resistance
eis 2715369 c.-37G>T upstream_gene_variant 0.13 kanamycin Assoc w R
ethA 4327480 c.-7T>C upstream_gene_variant 0.12 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 0.62 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.63 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.12 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.11 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.11 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 0.13 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.11 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 777451 p.Val344Leu missense_variant 0.59 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.55 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.1 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.5 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.11 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.68 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.57 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.53 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.14 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.31 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.55 pyrazinamide Uncertain significance
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 0.11 pyrazinamide Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.34 capreomycin
Rv2752c 3067147 c.-956A>T upstream_gene_variant 0.52 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 0.58 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.65 cycloserine
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.32 ethionamide
whiB7 3568605 c.75C>T synonymous_variant 0.33 kanamycin
amikacin
streptomycin Not assoc w R - Interim
Rv3236c 3612813 p.Thr102Ala missense_variant 0.11 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.68 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.13 rifampicin Not assoc w R
bedaquiline Uncertain significance
ddn 3987092 p.Glu83Asp missense_variant 0.57 pretomanid
delamanid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.13 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.11 ethambutol Not assoc w R
ethR 4327616 p.Asp23Gly missense_variant 0.53 ethionamide Uncertain significance
whiB6 4338563 c.-42G>T upstream_gene_variant 0.12 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 0.67 kanamycin
capreomycin
amikacin
gid 4407922 p.Leu94Pro missense_variant 0.54 streptomycin Uncertain significance
gid 4408213 c.-11C>T upstream_gene_variant 0.51 streptomycin Uncertain significance