TB-Profiler result

Run: SRR10808415
Summary

Run ID: SRR10808415

Sample name:

Date: 2024-04-15T00:25:17.132521

Number of reads: 2154001

Percentage reads mapped: 99.58

Median coverage: 67.0

Strain: lineage4.1.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.19
lineage4.1 Euro-American None 0.78
lineage4.1.2 Euro-American None 0.79
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.05
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.18
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 gid c.319dupG 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
gid 4407883 c.319dupG frameshift_variant 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 8040 p.Gly247Ser missense_variant 0.15 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 0.79 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.17 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.7 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.75 rifampicin Not assoc w R
rpoC 764263 c.894G>A synonymous_variant 0.78 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.11 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.77 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 781276 c.-284A>C upstream_gene_variant 0.17 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800200 c.-609C>G upstream_gene_variant 0.69 linezolid
Rv1129c 1253097 p.Ser480Pro missense_variant 0.78 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
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 0.83 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.27 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.24 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.17 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623170 p.Leu581Val missense_variant 0.81 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626416 c.198C>T synonymous_variant 0.68 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 0.11 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.13 ethambutol Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.12 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 0.78 ethambutol Not assoc w R
embB 4248705 p.Pro731Leu missense_variant 0.73 ethambutol 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
gid 4408070 p.Trp45Arg missense_variant 0.11 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.16 streptomycin Not assoc w R