TB-Profiler result

Run: SRR14807491
Summary

Run ID: SRR14807491

Sample name:

Date: 2024-04-15T10:16:18.957556

Number of reads: 4115414

Percentage reads mapped: 99.65

Median coverage: 132.0

Strain: lineage4.1.2.1;lineage4.8

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.29
lineage4.1.2 Euro-American None 0.32
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.28
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.69
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
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
rpsL 781822 p.Lys88Arg missense_variant 0.23 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.31 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.28 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13310 c.249T>C synonymous_variant 0.7 isoniazid Not assoc w R - Interim
fgd1 491424 c.650_655delCCGCTG disruptive_inframe_deletion 0.66 clofazimine
pretomanid
delamanid
fgd1 491591 p.Lys270Met missense_variant 0.31 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.28 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 575915 p.Asp190Asn missense_variant 0.65 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.38 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.35 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.37 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
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 1834675 c.1134C>T synonymous_variant 0.34 pyrazinamide
tsnR 1854204 p.Arg200Gln missense_variant 0.29 linezolid
tsnR 1854300 p.Leu232Pro missense_variant 0.29 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156219 c.-108A>T upstream_gene_variant 0.28 isoniazid Uncertain significance
PPE35 2168149 p.Pro822Ser missense_variant 0.73 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
kasA 2518076 c.-39C>T upstream_gene_variant 0.28 isoniazid
Rv2477c 2784541 c.-499G>A upstream_gene_variant 0.78 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.63 capreomycin
Rv2681 2997861 p.Pro375Ser missense_variant 0.28 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.29 cycloserine
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.71 ethionamide
lpqB 3624407 c.504C>T synonymous_variant 0.22 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.31 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878637 c.-130G>C upstream_gene_variant 0.26 rifampicin
embC 4239298 c.-565C>T upstream_gene_variant 0.31 ethambutol Not assoc w R
embC 4240373 c.511C>T synonymous_variant 0.74 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 0.29 ethambutol Not assoc w R
embA 4244849 c.1617C>T synonymous_variant 0.24 ethambutol Not assoc w R - Interim
embB 4246904 p.Val131Met missense_variant 0.71 ethambutol Uncertain significance
ubiA 4269192 c.642C>T synonymous_variant 0.69 ethambutol Not assoc w R - Interim
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 0.27 capreomycin
amikacin
kanamycin