TB-Profiler result

Run: SRR13232729
Summary

Run ID: SRR13232729

Sample name:

Date: 2024-03-24T16:51:15.409054

Number of reads: 4821313

Percentage reads mapped: 99.45

Median coverage: 155.0

Strain: lineage4.2.1.1;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 0.21
lineage4.2 Euro-American None 0.78
lineage4 Euro-American None 1.0
lineage4.2.1.1 Euro-American (TUR) None 0.78
lineage4.2.1 Euro-American (TUR) None 0.81
lineage4.3.3 Euro-American (LAM) RD115 0.21
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Gln497Arg Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Met175Ile Assoc w R - Interim
p.Asp49Gly Assoc w R
streptomycin rrs n.514A>C Assoc w R
n.517C>T Assoc w R
gid c.87delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine alr p.Leu113Arg Mutation from literature
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 761139 p.His445Asp missense_variant 0.14 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.85 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.21 streptomycin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.79 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.23 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288717 p.Met175Ile missense_variant 0.81 pyrazinamide Assoc w R - Interim
pncA 2289096 p.Asp49Gly missense_variant 0.12 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.18 kanamycin Assoc w R
alr 3841083 p.Leu113Arg missense_variant 0.24 cycloserine Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 0.15 ethambutol Uncertain significance Mutation from literature
embB 4248003 p.Gln497Arg missense_variant 0.25 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.78 ethambutol Uncertain significance Mutation from literature
gid 4408115 c.87delC frameshift_variant 0.74 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
dnaA 698 p.Arg233Gln missense_variant 0.2 isoniazid Uncertain significance
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 0.28 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 0.19 rifampicin Not assoc w R
rpoC 767123 p.Val1252Met missense_variant 0.86 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777451 p.Val344Leu missense_variant 0.8 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.81 linezolid
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.74 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.21 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304962 p.Trp678Gly missense_variant 0.21 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674102 c.-100C>A upstream_gene_variant 0.82 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834836 p.Met432Thr missense_variant 0.18 pyrazinamide Not assoc w R - Interim
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 2063685 c.1044G>A synonymous_variant 0.81 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.74 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.2 isoniazid Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.72 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 2518919 p.Gly269Ser missense_variant 0.2 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.22 para-aminosalicylic_acid
ribD 2986827 c.-12G>A upstream_gene_variant 1.0 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.25 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.77 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449006 p.His168Pro missense_variant 0.78 ethionamide Uncertain significance
Rv3236c 3612349 c.768A>C synonymous_variant 0.81 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
ddn 3987092 p.Glu83Asp missense_variant 0.86 delamanid Uncertain significance
pretomanid
clpC1 4038287 c.2418C>T synonymous_variant 0.22 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4327292 p.Thr61Arg missense_variant 0.8 ethionamide 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 4408156 p.Leu16Arg missense_variant 0.22 streptomycin Not assoc w R
gid 4408213 c.-11C>T upstream_gene_variant 0.81 streptomycin Uncertain significance