TB-Profiler result

Run: ERR13260895
Summary

Run ID: ERR13260895

Sample name:

Date: 2025-02-11T12:11:29.959850

Number of reads: 6408341

Percentage reads mapped: 99.59

Median coverage: 201.0

Strain: lineage2.2.2;lineage4.1.2.1

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
lineage2 East-Asian RD105 0.07
lineage4.1 Euro-American None 0.91
lineage4.1.2 Euro-American None 0.91
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.89
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.05
lineage2.2 East-Asian (Beijing) RD105;RD207 0.06
lineage4 Euro-American None 0.89
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
p.Ser441Leu Assoc w R
isoniazid
ethambutol
pyrazinamide pncA c.517dupG Assoc w R
streptomycin rrs n.514A>C Assoc w R
gid p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Asp94His Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94His Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine alr p.Leu113Arg Mutation from literature
ethionamide
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 7581 p.Asp94His missense_variant 0.12 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761110 p.Asp435Val missense_variant 0.13 rifampicin Assoc w R
rpoB 761128 p.Ser441Leu missense_variant 0.85 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.13 streptomycin Assoc w R
pncA 2288724 c.517dupG frameshift_variant 0.13 pyrazinamide Assoc w R
alr 3841083 p.Leu113Arg missense_variant 0.11 cycloserine Mutation from literature
gid 4407967 p.Leu79Ser missense_variant 0.14 streptomycin Uncertain significance Mutation from literature
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.89 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.1 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.83 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.87 ethionamide Uncertain significance
nusG 734444 p.Ala64Val missense_variant 0.95 rifampicin Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.93 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.93 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.89 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 777838 p.Ile215Val missense_variant 0.88 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781276 c.-284A>C upstream_gene_variant 0.9 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.91 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834655 p.Glu372Lys missense_variant 0.87 pyrazinamide 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
katG 2154724 p.Arg463Leu missense_variant 0.13 isoniazid 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.93 isoniazid
folC 2747796 c.-198C>T upstream_gene_variant 0.92 para-aminosalicylic_acid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.39 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.15 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.89 ethambutol Not assoc w R
embC 4242163 c.2301G>A synonymous_variant 0.87 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.93 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.12 ethambutol Not assoc w R
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
whiB6 4338794 c.-273A>G upstream_gene_variant 0.12 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.1 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.14 streptomycin Not assoc w R