TB-Profiler result

Run: ERR9119502
Summary

Run ID: ERR9119502

Sample name:

Date: 2024-04-16T10:17:24.779848

Number of reads: 5284545

Percentage reads mapped: 91.86

Median coverage: 157.0

Strain: lineage4.6.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.99
lineage4.6.2 Euro-American RD726 0.99
lineage4.6.2.2 Euro-American (Cameroon) RD726 1.0
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Ile6Thr Assoc w R
streptomycin gid c.102delG 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
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid Assoc w R High-level resistance
pncA 2289225 p.Ile6Thr missense_variant 1.0 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.98 ethambutol Assoc w R
gid 4408100 c.102delG 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 8129 c.828T>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8135 c.834C>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8177 c.876A>C synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8189 c.888G>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8198 c.897T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8207 c.906T>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778298 c.183G>A synonymous_variant 1.0 clofazimine Not assoc w R - Interim
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
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475028 n.1371G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
inhA 1673393 c.-809G>C upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834249 c.708T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834357 c.816T>G synonymous_variant 0.14 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834540 c.999G>T synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834546 c.1005T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834555 c.1014T>G synonymous_variant 0.15 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834666 c.1125G>C synonymous_variant 0.14 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 0.99 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063187 c.1542C>T synonymous_variant 0.99 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154980 p.Leu378Met missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2746320 p.Pro427Ala missense_variant 0.99 para-aminosalicylic_acid
Rv2477c 2783015 p.Ser343Thr missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783914 c.129T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783929 c.114C>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2996208 p.Ala35Asp missense_variant 1.0 capreomycin Uncertain significance
Rv3083 3448567 p.His22Asp missense_variant 1.0 ethionamide Uncertain significance
mtrB 3626930 c.-317A>G upstream_gene_variant 0.12 bedaquiline
rifampicin
ddn 3987011 c.168C>T synonymous_variant 1.0 delamanid Not assoc w R - Interim
pretomanid
clpC1 4039409 c.1296T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.13 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039454 c.1251A>G synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039466 c.1239T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039469 c.1236T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039481 c.1224T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039484 c.1221T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039589 c.1116G>T synonymous_variant 0.13 pyrazinamide
clpC1 4039622 c.1083C>T synonymous_variant 0.14 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 0.98 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 1.0 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 1.0 ethionamide 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 1.0 capreomycin
amikacin
kanamycin