TB-Profiler result

Run: SRR28393978
Summary

Run ID: SRR28393978

Sample name:

Date: 2024-05-22T08:35:32.053689

Number of reads: 20103138

Percentage reads mapped: 99.59

Median coverage: 575.0

Strain: lineage4.1.2.1;lineage4.3.3

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 0.24
lineage4.1 Euro-American None 0.76
lineage4.1.2 Euro-American None 0.75
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.75
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 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.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Lys48Thr Assoc w R - Interim
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA p.Pro378Leu Uncertain significance Mutation from literature
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 761110 p.Asp435Val missense_variant 0.2 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.34 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.22 isoniazid Assoc w R High-level resistance
pncA 2289099 p.Lys48Thr missense_variant 0.22 pyrazinamide Assoc w R - Interim
embB 4247429 p.Met306Val missense_variant 0.24 ethambutol Assoc w R
ethA 4326341 p.Pro378Leu missense_variant 0.25 ethionamide Uncertain significance Mutation from literature
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
dnaA 1053 c.1053C>T synonymous_variant 0.75 isoniazid 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 8040 p.Gly247Ser missense_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.8 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.77 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.76 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.74 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.25 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.78 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
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
rpsA 1833510 c.-31delG upstream_gene_variant 0.76 pyrazinamide 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
tlyA 1918164 c.225G>A synonymous_variant 0.74 capreomycin Not assoc w R - Interim
PPE35 2168590 p.Gln675Lys missense_variant 0.75 pyrazinamide Uncertain significance
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 0.74 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.26 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.19 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.23 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.24 pyrazinamide Not assoc w R
glpK 4139231 c.525A>G synonymous_variant 0.79 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4239298 c.-565C>T upstream_gene_variant 0.77 ethambutol Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.26 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 0.8 ethambutol Not assoc w R
embA 4243392 p.Asn54Asp missense_variant 0.26 ethambutol Uncertain significance
ubiA 4269731 p.Ala35Ser missense_variant 0.23 ethambutol Uncertain significance
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 4407986 p.Gly73Arg missense_variant 0.25 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.26 streptomycin Not assoc w R