TB-Profiler result

Run: ERR4821432
Summary

Run ID: ERR4821432

Sample name:

Date: 2024-10-05T12:42:54.381514

Number of reads: 3119988

Percentage reads mapped: 98.7

Median coverage: 65.0

Strain: lineage1.1.3.1;lineage4.1.3

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
lineage4.1.3 Euro-American None 0.88
lineage1.1.3 Indo-Oceanic RD239 0.14
lineage4.1 Euro-American None 0.87
lineage1.1 Indo-Oceanic RD239 0.09
lineage4 Euro-American None 0.91
lineage1 Indo-Oceanic RD239 0.1
lineage1.1.3.1 Indo-Oceanic RD239 0.13
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin gid p.Trp45* Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
inhA 1673425 c.-777C>T upstream_gene_variant 0.22 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gid 4408069 p.Trp45* stop_gained 0.13 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 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
gyrA 9557 c.2256G>C synonymous_variant 0.86 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13298 p.Ile87Met missense_variant 0.15 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.13 isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.75 ethionamide Uncertain significance
rpoC 763884 p.Ala172Val missense_variant 0.22 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.84 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.16 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.15 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 0.15 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 0.78 streptomycin Uncertain significance
fbiC 1304610 c.1680C>T synonymous_variant 0.9 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
embR 1417554 c.-207C>G upstream_gene_variant 0.16 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.18 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.29 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
tsnR 1853974 c.369C>T synonymous_variant 0.11 linezolid Not assoc w R
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
bacA 2062922 p.Ile603Val missense_variant 0.16 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.28 bedaquiline Not assoc w R - Interim
clofazimine 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
ahpC 2726051 c.-142G>A upstream_gene_variant 0.13 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.17 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623291 c.1620C>A synonymous_variant 0.9 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.13 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624660 p.Ala84Gly missense_variant 0.89 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841277 c.144C>T synonymous_variant 0.15 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.23 pyrazinamide Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 0.14 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.11 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.88 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.13 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.13 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
gid 4407588 c.615A>G synonymous_variant 0.1 streptomycin Not assoc w R