TB-Profiler result

Run: SRR12708376
Summary

Run ID: SRR12708376

Sample name:

Date: 2024-10-05T02:16:02.065099

Number of reads: 1318647

Percentage reads mapped: 99.41

Median coverage: 33.0

Strain: lineage2.2.1;lineage4.4.1.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.29
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.26
lineage2.2 East-Asian (Beijing) RD105;RD207 0.27
lineage4.4.1 Euro-American (S-type) None 0.63
lineage4 Euro-American None 0.76
lineage4.4.1.1 Euro-American None 0.7
lineage4.4 Euro-American None 0.69
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
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)
p.Ile194Thr Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA c.-12T>C Assoc w R
streptomycin rrs n.517C>T 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)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile194Thr Uncertain significance Mutation from literature
ethR p.Ala95Thr Uncertain significance Mutation from literature
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 7570 p.Ala90Val missense_variant 0.26 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)
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.21 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.52 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)
inhA 1674782 p.Ile194Thr missense_variant 0.34 ethionamide Uncertain significance Mutation from literature
isoniazid Uncertain significance Mutation from literature
pncA 2289253 c.-12T>C upstream_gene_variant 0.23 pyrazinamide Assoc w R
ethR 4327831 p.Ala95Thr missense_variant 0.32 ethionamide 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
gyrB 5462 p.Val75Leu missense_variant 0.81 levofloxacin
moxifloxacin
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 9138 p.Gln613Glu missense_variant 0.83 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 0.34 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.35 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.23 ethionamide Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.31 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 0.23 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777416 c.1065G>T synonymous_variant 0.65 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpS5 778979 c.-74G>T upstream_gene_variant 0.36 bedaquiline Not assoc w R - Interim
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.35 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
ndh 2102990 p.Val18Ala missense_variant 0.65 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.32 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.2 pyrazinamide Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.69 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.77 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 3065023 p.Pro390Leu missense_variant 0.67 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448522 p.Val7Phe missense_variant 0.75 ethionamide Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 0.71 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.48 kanamycin Not assoc w R
amikacin Not assoc w R
streptomycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.7 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.5 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877949 p.Thr187Ala missense_variant 0.23 rifampicin Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.86 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 0.41 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 0.21 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.23 streptomycin Not assoc w R