TB-Profiler result

Run: SRR25827509
Summary

Run ID: SRR25827509

Sample name:

Date: 2024-04-15T03:57:27.321458

Number of reads: 6794860

Percentage reads mapped: 98.81

Median coverage: 231.0

Strain: lineage2.2.1;lineage3;lineage4.3.2

Spoligotype:

Drug-resistance: MDR-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 0.3
lineage4.3 Euro-American (LAM) None 0.2
lineage2 East-Asian RD105 0.5
lineage4.3.2 Euro-American (LAM) None 0.2
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.51
lineage2.2 East-Asian (Beijing) RD105;RD207 0.5
lineage4 Euro-American None 0.19
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
rpoC p.Ile885Val Uncertain significance Mutation from literature
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.Asp354Ala Assoc w R
pyrazinamide pncA p.Phe106Ser Assoc w R - Interim
c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.514A>C Assoc w R
gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
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 761155 p.Ser450Leu missense_variant 0.86 rifampicin Assoc w R
rpoC 766022 p.Ile885Val missense_variant 0.26 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.29 streptomycin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.34 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.16 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 0.79 isoniazid Assoc w R High-level resistance
pncA 2288925 p.Phe106Ser missense_variant 0.25 pyrazinamide Assoc w R - Interim
pncA 2289252 c.-11A>G upstream_gene_variant 0.12 pyrazinamide Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.3 ethambutol Uncertain significance Mutation from literature
embB 4247574 p.Asp354Ala missense_variant 0.27 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.37 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7581 p.Asp94Cys missense_variant 0.16 levofloxacin
moxifloxacin
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 0.84 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.52 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.13 capreomycin Not assoc w R
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.55 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.79 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.51 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.26 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.26 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.77 rifampicin Not assoc w R
rpoC 764666 p.Gly433Ser missense_variant 0.16 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.13 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 0.8 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.44 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.54 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253394 p.Gln381Glu missense_variant 0.26 moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv1129c 1253930 p.Phe202Tyr missense_variant 0.17 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364489 p.Thr26Asn missense_variant 0.23 pyrazinamide
Rv1258c 1406760 c.580_581insC frameshift_variant 0.49 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417046 p.Tyr101Cys missense_variant 0.19 ethambutol
embR 1417284 p.Thr22Ala missense_variant 0.27 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.21 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.43 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 0.82 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.77 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
pncA 2289365 c.-125delC upstream_gene_variant 0.33 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.29 isoniazid Not assoc w R
folC 2747468 p.Asp44Gly missense_variant 0.26 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.29 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
thyA 3073868 p.Thr202Ala missense_variant 0.15 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.49 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626220 p.Met132Val missense_variant 0.26 bedaquiline
rifampicin
mtrB 3626562 p.Pro18Ser missense_variant 0.51 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640330 c.-213C>T upstream_gene_variant 0.2 clofazimine
pretomanid
delamanid
fbiA 3640331 c.-212T>G upstream_gene_variant 0.2 clofazimine
pretomanid
delamanid
fbiB 3642877 p.Lys448Arg missense_variant 0.22 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rpoA 3878417 p.Gly31Ser missense_variant 0.28 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.17 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.28 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.27 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139246 c.510C>T synonymous_variant 0.33 ethambutol Not assoc w R
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
embC 4241022 p.Ala387Val missense_variant 0.15 ethambutol Uncertain significance
embC 4241353 p.Ile497Met missense_variant 0.2 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.3 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 0.46 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.17 ethambutol
embB 4247717 p.Leu402Val missense_variant 0.3 ethambutol Uncertain significance
embB 4249757 p.Thr1082Ala missense_variant 0.34 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.47 ethambutol Not assoc w R
ethA 4326224 p.Val417Gly missense_variant 0.3 ethionamide
whiB6 4338293 p.Ala77Thr missense_variant 0.28 capreomycin
amikacin
kanamycin
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 0.99 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.8 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.13 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.51 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.15 streptomycin Not assoc w R