TB-Profiler result

Run: SRR22528530
Summary

Run ID: SRR22528530

Sample name:

Date: 2024-10-04T15:37:56.323079

Number of reads: 1308759

Percentage reads mapped: 99.65

Median coverage: 42.0

Strain: lineage4.1.2.1;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
lineage4.1 Euro-American None 0.75
lineage4.1.2 Euro-American None 0.75
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.71
lineage4.4.1 Euro-American (S-type) None 0.31
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 0.24
lineage4.4 Euro-American None 0.24
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
pyrazinamide
streptomycin rpsL p.Lys43Arg 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 0.28 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.28 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
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 8116 p.Thr272Ile missense_variant 0.39 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13634 c.-76G>A upstream_gene_variant 0.36 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.91 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.8 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.67 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.64 rifampicin Not assoc w R
rpoB 761528 p.Asp574Glu missense_variant 0.38 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.7 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
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
ndh 2102990 p.Val18Ala missense_variant 0.31 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.72 isoniazid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.17 capreomycin Uncertain significance
thyA 3074495 c.-24C>T upstream_gene_variant 0.17 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.37 ethionamide Not assoc w R - Interim
Rv3236c 3612665 p.Val151Ala missense_variant 0.36 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625771 c.843C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
bedaquiline
embC 4238963 c.-900C>T upstream_gene_variant 0.24 ethambutol Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.67 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 0.58 ethambutol Not assoc w R
embA 4244970 c.1738C>T synonymous_variant 0.23 ethambutol Not assoc w R - Interim
whiB6 4338514 p.Tyr3Cys missense_variant 0.24 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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 4408157 p.Leu16Val missense_variant 0.31 streptomycin