TB-Profiler result

Run: ERR9786245
Summary

Run ID: ERR9786245

Sample name:

Date: 2024-04-15T04:56:54.432528

Number of reads: 1986503

Percentage reads mapped: 99.78

Median coverage: 103.0

Strain: lineage4.3.4.2;lineage4.6.2.2

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 0.47
lineage4.6 Euro-American None 0.52
lineage4.6.2 Euro-American RD726 0.56
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.53
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.45
lineage4.3.4.2 Euro-American (LAM) RD174 0.49
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 fbiC c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Assoc w R - Interim
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
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 0.99 pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
delamanid Assoc w R - Interim
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 6817 c.1578G>A synonymous_variant 0.41 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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
rpoC 764995 c.1626C>G synonymous_variant 0.4 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 778298 c.183G>A synonymous_variant 0.54 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
embR 1417258 c.90G>A synonymous_variant 0.42 ethambutol Not assoc w R - Interim
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
bacA 2063187 c.1542C>T synonymous_variant 0.54 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2155389 c.723C>G synonymous_variant 0.46 isoniazid Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.5 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
Rv2680 2996208 p.Ala35Asp missense_variant 0.46 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 0.48 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.54 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.41 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.58 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.44 pyrazinamide Not assoc w R
Rv3236c 3612571 c.546C>T synonymous_variant 0.55 pyrazinamide Not assoc w R
lpqB 3624739 p.Ala58Ser missense_variant 0.59 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.49 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.48 pyrazinamide Not assoc w R
embC 4239763 c.-100C>T upstream_gene_variant 0.49 ethambutol Not assoc w R
embC 4242550 c.2688C>G synonymous_variant 0.57 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245745 p.Pro838Leu missense_variant 0.46 ethambutol Uncertain significance
aftB 4267272 p.Lys522Arg missense_variant 0.58 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 0.53 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.58 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
gid 4408156 p.Leu16Arg missense_variant 0.45 streptomycin Not assoc w R