TB-Profiler result

Run: SRR25827582
Summary

Run ID: SRR25827582

Sample name:

Date: 2024-10-04T10:19:41.413202

Number of reads: 6927949

Percentage reads mapped: 99.2

Median coverage: 238.0

Strain: lineage3;lineage4.8

Spoligotype:

Drug-resistance: 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 0.48
lineage4 Euro-American None 0.56
lineage4.8 Euro-American (mainly T) RD219 0.54
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.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. 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.-16C>T Uncertain significance Mutation from literature
c.-11C>A Uncertain significance Mutation from literature
embB p.Met306Thr Uncertain significance Mutation from literature
pyrazinamide pncA p.Trp68Gly Assoc w R
p.Asp8Tyr Assoc w R - Interim
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala 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.Asp94Ala Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid rplC p.Cys154Arg Assoc w R
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.Asp94Ala missense_variant 0.52 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 0.48 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.41 linezolid Assoc w R
inhA 1673432 c.-770T>C upstream_gene_variant 0.47 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289040 p.Trp68Gly missense_variant 0.51 pyrazinamide Assoc w R
pncA 2289220 p.Asp8Tyr missense_variant 0.48 pyrazinamide Assoc w R - Interim
eis 2715342 c.-10G>A upstream_gene_variant 0.44 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embA 4243217 c.-16C>T upstream_gene_variant 0.39 ethambutol Uncertain significance Mutation from literature
embA 4243222 c.-11C>A upstream_gene_variant 0.61 ethambutol Uncertain significance Mutation from literature
embB 4247430 p.Met306Thr missense_variant 0.44 ethambutol Uncertain significance Mutation from literature
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 0.48 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.45 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.54 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.53 ethionamide Not assoc w R - Interim
nusG 734658 c.405A>G synonymous_variant 0.57 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.45 rifampicin Not assoc w R
rpoB 760719 p.Val305Ile missense_variant 0.44 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.53 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.41 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.47 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 0.42 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.44 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.49 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1475636 n.1979A>G non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.47 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102978 p.Ser22Phe missense_variant 0.46 isoniazid Uncertain significance
delamanid
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.49 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.42 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.53 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
pncA 2289047 c.195C>T synonymous_variant 0.47 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.38 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.51 isoniazid Not assoc w R
folC 2747481 p.Glu40Lys missense_variant 0.43 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.48 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2477c 2784209 c.-167G>C upstream_gene_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.43 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.48 cycloserine
Rv3083 3448460 c.-43delA upstream_gene_variant 0.3 ethionamide Uncertain significance
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.5 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.48 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640527 c.-16G>A upstream_gene_variant 0.54 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
alr 3840520 p.Ala301Ser missense_variant 0.47 cycloserine
alr 3841473 c.-53G>A upstream_gene_variant 0.42 cycloserine
clpC1 4039729 p.Asp326Asn missense_variant 0.59 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.46 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.5 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.54 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.18 ethambutol
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 0.47 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.38 streptomycin Not assoc w R
gid 4407901 p.Leu101Arg missense_variant 0.45 streptomycin Uncertain significance
gid 4407955 p.Arg83Gln missense_variant 0.48 streptomycin Uncertain significance
gid 4408006 p.Val66Gly missense_variant 0.52 streptomycin
gid 4408335 c.-133A>G upstream_gene_variant 0.52 streptomycin