TB-Profiler result

Run: SRR25827607
Summary

Run ID: SRR25827607

Sample name:

Date: 2024-10-05T00:01:54.920095

Number of reads: 3161648

Percentage reads mapped: 50.0

Median coverage: 91.0

Strain: lineage2.2.1;lineage4.8

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 0.55
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.53
lineage2.2 East-Asian (Beijing) RD105;RD207 0.58
lineage4 Euro-American None 0.41
lineage4.8 Euro-American (mainly T) RD219 0.42
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 embA c.-11C>A Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
p.Gln497Lys Assoc w R
pyrazinamide pncA p.Val155Met Assoc w R
p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Gly88Cys Assoc w R High-level resistance
p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Gly88Cys Assoc w R
p.Ala90Val 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
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 7563 p.Gly88Cys missense_variant 0.38 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
gyrA 7570 p.Ala90Val missense_variant 0.58 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)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.62 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 0.99 isoniazid Assoc w R High-level resistance
pncA 2288779 p.Val155Met missense_variant 0.33 pyrazinamide Assoc w R
pncA 2289162 p.Leu27Pro missense_variant 0.79 pyrazinamide Assoc w R
embA 4243222 c.-11C>A upstream_gene_variant 0.57 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.54 ethambutol Assoc w R
embB 4248002 p.Gln497Lys missense_variant 0.37 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
gyrB 5332 c.93C>T synonymous_variant 0.32 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.61 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8168 p.Glu289Asp missense_variant 0.35 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9304 p.Gly668Asp missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.66 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.51 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.36 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.71 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.72 ethionamide Uncertain significance
hadA 731865 c.-65C>T upstream_gene_variant 0.78 isoniazid
nusG 734658 c.405A>G synonymous_variant 0.48 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.52 rifampicin Not assoc w R
rpoC 765612 p.His748Pro missense_variant 0.41 rifampicin Uncertain significance
rpoC 766488 p.Pro1040Arg missense_variant 0.62 rifampicin Uncertain significance
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 0.59 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.57 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.66 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.52 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 0.72 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.43 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 0.65 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.59 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.3 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.46 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.73 cycloserine
whiB7 3568435 c.242_245delGTCCinsATCCTT frameshift_variant&missense_variant 0.75 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3568442 p.Lys80Gln missense_variant 0.63 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3568443 p.His79Gln missense_variant 0.59 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3568854 c.-176delG upstream_gene_variant 0.6 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3569220 c.-541C>T upstream_gene_variant 0.66 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.51 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.37 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.53 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.6 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.37 pyrazinamide 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 0.42 ethambutol Not assoc w R
embA 4245417 p.Gly729Arg missense_variant 0.44 ethambutol Uncertain significance
embB 4247028 p.Leu172Arg missense_variant 0.22 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.49 ethambutol Not assoc w R
ubiA 4269298 p.Ile179Thr missense_variant 0.34 ethambutol Uncertain significance
ethA 4326513 p.Thr321Pro missense_variant 0.68 ethionamide Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 0.67 ethionamide Uncertain significance
ethA 4327301 p.Asp58Gly missense_variant 0.4 ethionamide Uncertain significance
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 0.73 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.51 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.53 streptomycin Not assoc w R