TB-Profiler result

Run: SRR28351216
Summary

Run ID: SRR28351216

Sample name:

Date: 2024-10-03T14:27:29.247325

Number of reads: 9665222

Percentage reads mapped: 99.86

Median coverage: 278.0

Strain: lineage4.2.1

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
lineage4.2 Euro-American None 0.31
lineage4 Euro-American None 0.33
lineage4.2.1 Euro-American (TUR) None 0.34
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.Asn296His Uncertain significance Mutation from literature
p.Ser297Ala Uncertain significance Mutation from literature
p.Met306Ile Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Thr47Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
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
capreomycin
kanamycin eis c.-12C>T 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 0.64 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.6 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.26 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.22 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 0.92 isoniazid Assoc w R High-level resistance
pncA 2289103 p.Thr47Ala missense_variant 0.46 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.2 kanamycin Assoc w R
embB 4247399 p.Asn296His missense_variant 0.16 ethambutol Uncertain significance Mutation from literature
embB 4247402 p.Ser297Ala missense_variant 0.22 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.15 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.22 ethambutol Uncertain significance Mutation from literature
ethA 4327033 p.Tyr147* stop_gained 0.35 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 491247 c.465C>T synonymous_variant 0.31 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.51 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.82 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.15 kanamycin Uncertain significance
capreomycin Not assoc w R - Interim
amikacin Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.77 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.5 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.51 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.52 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.46 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.47 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.58 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 0.78 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.77 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpR5 779183 p.Gly65Val missense_variant 0.14 bedaquiline
clofazimine
mmpS5 779615 c.-710C>G upstream_gene_variant 0.67 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.38 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254593 c.-60dupA upstream_gene_variant 0.35 levofloxacin
moxifloxacin
isoniazid
rifampicin
sigE 1364706 c.294G>A synonymous_variant 0.6 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75 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 0.63 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 0.99 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.34 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.29 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.71 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.35 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.64 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086742 c.-78A>C upstream_gene_variant 0.5 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.66 pyrazinamide Not assoc w R - Interim
lpqB 3623222 c.1689A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
bedaquiline 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 0.83 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4243225 c.-8C>A upstream_gene_variant 0.54 ethambutol Uncertain significance
embA 4243346 c.114A>G synonymous_variant 0.15 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.85 ethambutol Not assoc w R
embA 4245812 c.2580G>A synonymous_variant 0.37 ethambutol Not assoc w R - Interim
embB 4247507 p.Trp332Arg missense_variant 0.44 ethambutol Uncertain significance
embB 4249594 c.3081G>A synonymous_variant 0.23 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.77 ethambutol Not assoc w R
ethA 4326632 p.His281Pro missense_variant 0.56 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.27 ethionamide
whiB6 4338371 p.Thr51Pro missense_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
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 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.49 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.6 streptomycin Not assoc w R