TB-Profiler result

Run: SRR29093366
Summary

Run ID: SRR29093366

Sample name:

Date: 2024-10-03T14:49:21.639798

Number of reads: 2631928

Percentage reads mapped: 99.43

Median coverage: 79.0

Strain: lineage2.2.2;lineage4.4.2

Spoligotype:

Drug-resistance: 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 0.76
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.74
lineage2.2 East-Asian (Beijing) RD105;RD207 0.79
lineage4 Euro-American None 0.22
lineage4.4 Euro-American None 0.23
lineage4.4.2 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.His445Asp 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)
c.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ala379Val Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Lys96Arg Assoc w R
streptomycin gid c.517dupG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val 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.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine alr p.Met343Thr Mutation from literature
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
ethA p.Trp116* Assoc w R
clofazimine
para-aminosalicylic_acid folC p.Ile43Thr Mutation from literature
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 7570 p.Ala90Val missense_variant 0.81 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 0.81 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Asp missense_variant 0.81 rifampicin Assoc w R
rplC 801268 p.Cys154Arg missense_variant 0.32 linezolid Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.7 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673432 c.-770T>C upstream_gene_variant 0.86 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)
inhA 1674048 c.-154G>A upstream_gene_variant 0.31 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2154976 p.Ala379Val missense_variant 0.75 isoniazid Uncertain significance Mutation from literature
pncA 2288955 p.Lys96Arg missense_variant 0.73 pyrazinamide Assoc w R
folC 2747471 p.Ile43Thr missense_variant 0.78 para-aminosalicylic_acid Mutation from literature
alr 3840393 p.Met343Thr missense_variant 0.78 cycloserine Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.67 ethambutol Assoc w R
ethA 4327126 p.Trp116* stop_gained 0.85 ethionamide Assoc w R
gid 4407685 c.517dupG frameshift_variant 0.68 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
dnaA 796 p.Asp266Asn missense_variant 0.87 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.99 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 0.86 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.78 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.77 ethionamide Uncertain significance
mmaA3 737988 c.162A>G synonymous_variant 0.27 isoniazid
rpoB 760075 p.Ile90Ser missense_variant 0.83 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.83 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 0.7 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.78 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781406 c.-154_-153insC upstream_gene_variant 0.71 streptomycin Uncertain significance
Rv1129c 1254136 p.Glu133Asp missense_variant 0.64 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.85 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 1475951 n.2294G>A non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid
rpsA 1833909 p.Asp123Ala missense_variant 0.8 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.91 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 0.89 isoniazid Not assoc w R
katG 2155602 p.Asn170Lys missense_variant 0.78 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.79 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
Rv2752c 3066099 p.Met31Ile missense_variant 0.2 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.26 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.85 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3841356 p.Ser22Leu missense_variant 0.81 cycloserine
clpC1 4040722 c.-18G>A upstream_gene_variant 0.75 pyrazinamide
glpK 4139183 c.572dupG frameshift_variant 0.19 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.34 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 0.64 ethambutol Not assoc w R
embA 4246508 c.3276G>A synonymous_variant 0.42 ethambutol Not assoc w R
embB 4247989 c.1476G>A synonymous_variant 0.29 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.69 ethambutol Not assoc w R
ubiA 4268928 c.906C>T synonymous_variant 0.26 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.26 ethambutol 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 0.8 streptomycin Not assoc w R
gid 4407766 p.Thr146Lys missense_variant 0.32 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.77 streptomycin Not assoc w R
gid 4408366 c.-164C>T upstream_gene_variant 0.2 streptomycin