TB-Profiler result

Run: SRR13583385
Summary

Run ID: SRR13583385

Sample name:

Date: 2024-10-05T10:19:06.236297

Number of reads: 2439695

Percentage reads mapped: 99.12

Median coverage: 72.0

Strain: lineage4.3.4.1;lineage4.4.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.53
lineage4.3.4.1 Euro-American (LAM) RD174 0.55
lineage4.4.1 Euro-American (S-type) None 0.42
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.43
lineage4.3.4 Euro-American (LAM) RD174 0.57
lineage4.4 Euro-American None 0.41
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu452Pro Assoc w R
isoniazid katG c.1086_1089dupCACC Assoc w R High-level resistance
c.1080delT Assoc w R High-level resistance
p.Ser315Thr Assoc w R High-level resistance
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
rpoB 761161 p.Leu452Pro missense_variant 0.67 rifampicin Assoc w R
katG 2155022 c.1086_1089dupCACC frameshift_variant 0.27 isoniazid Assoc w R High-level resistance
katG 2155031 c.1080delT frameshift_variant 0.29 isoniazid Assoc w R High-level resistance
katG 2155168 p.Ser315Thr missense_variant 0.64 isoniazid Assoc w R High-level resistance
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 4988 c.-252C>G upstream_gene_variant 0.57 levofloxacin
moxifloxacin
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 8715 p.Pro472Ser missense_variant 0.66 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 759608 c.-199C>T upstream_gene_variant 0.53 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.56 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
sigE 1364434 p.Arg8Trp missense_variant 0.49 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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 2063865 c.864C>T synonymous_variant 0.36 kanamycin
capreomycin
streptomycin Not assoc w R - Interim
amikacin
ndh 2102990 p.Val18Ala missense_variant 0.45 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2169840 p.Gly258Asp missense_variant 0.44 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714914 c.418delC frameshift_variant 0.43 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2726323 p.Pro44Arg missense_variant 0.43 isoniazid Uncertain significance
pepQ 2859830 p.Gly197Arg missense_variant 0.66 bedaquiline Uncertain significance
clofazimine Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.66 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448598 p.Ile32Thr missense_variant 0.62 ethionamide Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 0.35 ethionamide Not assoc w R - Interim
Rv3236c 3612009 p.Ala370Thr missense_variant 0.59 pyrazinamide Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.52 pyrazinamide Not assoc w R
Rv3236c 3612768 p.Ala117Pro missense_variant 0.55 pyrazinamide Uncertain significance
lpqB 3623841 p.Gln357Leu missense_variant 0.45 rifampicin Uncertain significance
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.54 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.42 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 0.45 streptomycin Not assoc w R