TB-Profiler result

Run: SRR1163446
Summary

Run ID: SRR1163446

Sample name:

Date: 2024-10-03T22:29:14.110288

Number of reads: 6930283

Percentage reads mapped: 99.41

Median coverage: 146.0

Strain: lineage2.2.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.49
lineage4.1 Euro-American None 0.52
lineage4.1.2 Euro-American None 0.52
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.48
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.51
lineage2.2 East-Asian (Beijing) RD105;RD207 0.5
lineage4 Euro-American None 0.49
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Tyr 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 embB p.Gly406Asp Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Thr76Pro Assoc w R
c.-5_7delGACGTATGCGGG Assoc w R
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Tyr147* Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.11 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761109 p.Asp435Tyr missense_variant 0.34 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.57 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.49 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.93 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.57 ethionamide Assoc w R Alias fabG1_c.-15C>T
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)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289016 p.Thr76Pro missense_variant 0.43 pyrazinamide Assoc w R
pncA 2289234 c.-5_7delGACGTATGCGGG frameshift_variant&start_lost 0.51 pyrazinamide Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.37 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.46 ethambutol Assoc w R
ethA 4327033 p.Tyr147* stop_gained 0.37 ethionamide 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
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
fgd1 491591 p.Lys270Met missense_variant 0.57 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.5 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.5 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.42 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.57 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.46 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.45 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.5 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.59 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.58 rifampicin Not assoc w R
rpoB 760320 p.Gln172Lys missense_variant 0.53 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.48 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.48 rifampicin Uncertain significance
rpoC 764923 p.Glu518Asp missense_variant 0.14 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.47 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.48 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.44 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.57 bedaquiline
clofazimine
rpsL 781276 c.-284A>C upstream_gene_variant 0.46 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.46 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.61 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.46 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.61 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
katG 2154724 p.Arg463Leu missense_variant 0.52 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.56 pyrazinamide Not assoc w R
PPE35 2169016 p.Thr533Ala missense_variant 0.41 pyrazinamide 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 0.49 isoniazid
folC 2746747 c.852G>C synonymous_variant 0.5 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.48 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.53 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.57 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 0.5 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.46 ethambutol Not assoc w R
embB 4248706 c.2193G>A synonymous_variant 0.43 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.5 ethambutol Not assoc w R
ethA 4326864 p.Met204Val missense_variant 0.54 ethionamide Uncertain significance
whiB6 4338513 c.9C>T synonymous_variant 0.45 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
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 0.99 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.46 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.58 streptomycin Not assoc w R