TB-Profiler result

Run: SRR3105742
Summary

Run ID: SRR3105742

Sample name:

Date: 2024-04-16T08:31:04.208902

Number of reads: 1471274

Percentage reads mapped: 98.44

Median coverage: 28.0

Strain: lineage2.2.1;lineage3

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
lineage3 East-African-Indian RD750 0.44
lineage2 East-Asian RD105 0.55
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.57
lineage2.2 East-Asian (Beijing) RD105;RD207 0.61
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
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
p.Pro404Ser Uncertain significance Mutation from literature
pyrazinamide pncA c.391dupG Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Asp461Asn Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Asp461Asn Assoc w R
gyrA p.Ala90Val Assoc w R
p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.926dupA 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
gyrB 6620 p.Asp461Asn missense_variant 0.38 levofloxacin Assoc w R
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7570 p.Ala90Val missense_variant 0.48 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Ala missense_variant 0.52 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761109 p.Asp435Tyr missense_variant 0.65 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.79 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.7 isoniazid Assoc w R High-level resistance
pncA 2288850 c.391dupG frameshift_variant 0.3 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.43 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.47 ethambutol Assoc w R
embB 4247723 p.Pro404Ser missense_variant 0.61 ethambutol Uncertain significance Mutation from literature
ethA 4326547 c.926dupA frameshift_variant 0.5 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
dnaA 845 p.Ile282Thr missense_variant 0.59 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.47 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.8 ethionamide Uncertain significance
Rv0565c 657263 c.207delT frameshift_variant 0.39 ethionamide Uncertain significance
rpoB 760321 p.Gln172Arg missense_variant 0.4 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.42 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.95 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.53 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpR5 779048 p.Val20Ala missense_variant 0.42 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.71 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.48 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 1.0 isoniazid Not assoc w R
katG 2155653 p.Lys153Asn missense_variant 0.46 isoniazid Uncertain significance
katG 2155724 p.Ala130Thr missense_variant 0.45 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.94 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726105 c.-88G>A upstream_gene_variant 0.48 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.33 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
pepQ 2860572 c.-154G>A upstream_gene_variant 0.45 clofazimine
bedaquiline
ald 3086788 c.-32T>C upstream_gene_variant 0.97 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.63 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.57 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.48 pyrazinamide
embC 4242075 p.Arg738Gln missense_variant 0.38 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.61 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.5 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.48 ethambutol Not assoc w R
aftB 4269564 c.-728G>A upstream_gene_variant 0.53 ethambutol
ethA 4327132 p.Asn114Lys missense_variant 0.36 ethionamide
whiB6 4338286 c.235delG frameshift_variant 0.26 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.45 streptomycin Not assoc w R
gid 4408018 p.Gly62Val missense_variant 0.57 streptomycin Uncertain significance
gid 4408168 p.Phe12Cys missense_variant 0.4 streptomycin Uncertain significance