TB-Profiler result

Run: SRR5073947
Summary

Run ID: SRR5073947

Sample name:

Date: 2024-03-26T14:53:17.727425

Number of reads: 3771468

Percentage reads mapped: 99.4

Median coverage: 117.0

Strain: lineage1.1.1.1;lineage4.5

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.9
lineage1.1 Indo-Oceanic RD239 0.07
lineage4 Euro-American None 0.94
lineage1 Indo-Oceanic RD239 0.06
lineage1.1.1.1 Indo-Oceanic RD239 0.07
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)
p.Ile21Thr Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin gid c.115delC 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
p.Ile21Thr Uncertain significance Mutation from literature
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 0.9 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
inhA 1674263 p.Ile21Thr missense_variant 0.94 isoniazid Uncertain significance Mutation from literature
ethionamide Uncertain significance Mutation from literature
gid 4408087 c.115delC frameshift_variant 1.0 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 7892 c.591G>A synonymous_variant 0.84 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9143 c.1842T>C synonymous_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 13394 p.Trp55* stop_gained 0.94 isoniazid Uncertain significance
ccsA 620029 c.139C>T synonymous_variant 0.89 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.11 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.11 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.15 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
fbiC 1302778 c.-153G>A upstream_gene_variant 0.88 clofazimine
pretomanid
delamanid
embR 1417554 c.-207C>G upstream_gene_variant 0.1 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.11 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1853850 p.Thr82Lys missense_variant 0.91 linezolid Uncertain significance
tsnR 1854045 p.Tyr147Cys missense_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
katG 2155751 p.Gly121Ser missense_variant 0.92 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.11 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.12 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.92 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
Rv2477c 2782423 c.1620C>T synonymous_variant 0.92 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.19 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.12 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624893 c.18G>A synonymous_variant 0.93 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878336 p.Gly58Arg missense_variant 0.91 rifampicin Uncertain significance
rpoA 3879070 c.-563G>A upstream_gene_variant 0.93 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.88 pyrazinamide Not assoc w R
embC 4242095 p.Ala745Thr missense_variant 0.89 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.11 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.12 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 1.0 capreomycin
amikacin
kanamycin