TB-Profiler result

Run: SRR25827769
Summary

Run ID: SRR25827769

Sample name:

Date: 2024-04-14T13:47:21.144396

Number of reads: 9202125

Percentage reads mapped: 98.82

Median coverage: 307.0

Strain: lineage2.2.1;lineage4.5

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
lineage4.5 Euro-American RD122 0.52
lineage2 East-Asian RD105 0.45
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.43
lineage2.2 East-Asian (Beijing) RD105;RD207 0.46
lineage4 Euro-American None 0.51
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
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.Met306Val Assoc w R
pyrazinamide pncA p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp89Asn Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp89Asn Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
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 7566 p.Asp89Asn missense_variant 0.53 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.Asp94Gly missense_variant 0.29 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.5 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.46 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.51 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 0.47 isoniazid Assoc w R High-level resistance
pncA 2289228 p.Ile5Ser missense_variant 0.14 pyrazinamide Assoc w R
thyA 3074408 p.Thr22Ala missense_variant 0.15 para-aminosalicylic_acid Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.23 ethambutol 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 7892 c.591G>A synonymous_variant 0.5 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490998 c.216T>G synonymous_variant 0.47 clofazimine
pretomanid
delamanid
fgd1 491290 p.Val170Met missense_variant 0.15 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.46 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.47 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 576651 p.Asp435Ala missense_variant 0.25 ethionamide
isoniazid
mshA 576657 p.Leu437Arg missense_variant 0.17 ethionamide
isoniazid
ccsA 620029 c.139C>T synonymous_variant 0.45 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620553 c.663T>C synonymous_variant 0.23 capreomycin Not assoc w R
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.42 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.45 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.4 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.48 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.18 rifampicin Uncertain significance
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 0.45 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.41 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.45 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 0.49 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1304207 p.Arg426His missense_variant 0.44 clofazimine
pretomanid
delamanid
Rv1258c 1406101 p.Pro414Ser missense_variant 0.52 streptomycin Uncertain significance
isoniazid Not assoc w R
pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.43 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834078 c.537C>T synonymous_variant 0.54 pyrazinamide
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 0.5 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.51 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.49 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
thyX 3067949 c.-4C>T upstream_gene_variant 0.21 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.46 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.48 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 0.46 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640211 c.-332T>G upstream_gene_variant 0.22 clofazimine
pretomanid
delamanid
rpoA 3878575 c.-68C>T upstream_gene_variant 0.8 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.43 pyrazinamide Not assoc w R
clpC1 4039439 c.1266C>T synonymous_variant 0.52 pyrazinamide
embC 4241022 p.Ala387Val missense_variant 0.16 ethambutol Uncertain significance
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
embA 4245835 p.Leu868Arg missense_variant 0.21 ethambutol
embB 4247015 p.Ser168Ala missense_variant 0.27 ethambutol
embB 4249757 p.Thr1082Ala missense_variant 0.23 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.25 ethambutol Not assoc w R
ethA 4326626 p.Gly283Asp missense_variant 0.5 ethionamide
whiB6 4338292 p.Ala77Val missense_variant 0.2 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338365 p.Cys53Arg missense_variant 0.53 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 0.5 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.15 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.44 streptomycin Not assoc w R