TB-Profiler result

Run: ERR11465234
Summary

Run ID: ERR11465234

Sample name:

Date: 2024-04-14T23:04:15.000636

Number of reads: 4075620

Percentage reads mapped: 99.11

Median coverage: 124.0

Strain: lineage4.1.2.1;lineage4.3.4.2.1

Spoligotype:

Drug-resistance: Sensitive

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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 0.21
lineage4.1 Euro-American None 0.77
lineage4.1.2 Euro-American None 0.78
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.76
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.23
lineage4.3.4 Euro-American (LAM) RD174 0.22
lineage4.3.4.2 Euro-American (LAM) RD174 0.21
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
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
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
gyrB 6140 p.Val301Leu missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 7592 c.291G>C synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.77 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.78 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.24 ethionamide
isoniazid
Rv0565c 656340 p.Met377Ile missense_variant 0.81 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.75 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.72 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.71 rifampicin Not assoc w R
rpoC 764056 c.687G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764059 c.690G>C synonymous_variant 0.11 rifampicin
rpoC 764134 c.765C>G synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764143 c.774G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764147 p.Ser260Ala missense_variant 0.11 rifampicin Uncertain significance
rpoC 764347 c.978G>C synonymous_variant 0.11 rifampicin
rpoC 764353 c.984G>T synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764410 c.1041G>C synonymous_variant 0.11 rifampicin
rpoC 764431 c.1062G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764449 c.1080G>C synonymous_variant 0.15 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.14 rifampicin
rpoC 764455 c.1086G>A synonymous_variant 0.15 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764485 c.1116G>C synonymous_variant 0.16 rifampicin
rpoC 764491 c.1122G>T synonymous_variant 0.17 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764500 c.1131C>G synonymous_variant 0.19 rifampicin
rpoC 764503 c.1134G>T synonymous_variant 0.19 rifampicin
rpoC 764510 c.1141C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>T synonymous_variant 0.16 rifampicin
rpoC 764536 c.1167G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>A synonymous_variant 0.24 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.84 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.8 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.79 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid 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
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 0.78 isoniazid
Rv2680 2996136 p.Ser11Asn missense_variant 0.12 capreomycin
thyX 3067248 p.Thr233Ile missense_variant 0.31 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.24 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.19 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 0.23 cycloserine
rpoA 3877797 c.711G>C synonymous_variant 0.11 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 0.24 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.7 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 0.69 ethambutol Not assoc w R
embA 4243608 p.Ala126Ser missense_variant 0.85 ethambutol
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 4408156 p.Leu16Arg missense_variant 0.21 streptomycin Not assoc w R