TB-Profiler result

Run: ERR10748138
Summary

Run ID: ERR10748138

Sample name:

Date: 2024-04-16T01:55:10.452578

Number of reads: 1180358

Percentage reads mapped: 99.9

Median coverage: 50.0

Strain: lineage2.2.2;lineage4.4.1.1

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
lineage2 East-Asian RD105 0.46
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.46
lineage2.2 East-Asian (Beijing) RD105;RD207 0.47
lineage4.4.1 Euro-American (S-type) None 0.55
lineage4 Euro-American None 0.52
lineage4.4.1.1 Euro-American None 0.53
lineage4.4 Euro-American None 0.52
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>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
pyrazinamide pncA c.517dupG Assoc w R
c.62delT Assoc w R
streptomycin rrs n.514A>C Assoc w R
gid p.Leu79Ser Uncertain significance Mutation from literature
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 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.Leu113Arg Mutation from literature
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
ethA p.Ala381Pro 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 0.54 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761110 p.Asp435Val missense_variant 0.43 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.52 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.61 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.68 kanamycin Assoc w R
capreomycin Assoc w R
amikacin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.4 isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288724 c.517dupG frameshift_variant 0.47 pyrazinamide Assoc w R
pncA 2289179 c.62delT frameshift_variant 0.63 pyrazinamide Assoc w R
alr 3841083 p.Leu113Arg missense_variant 0.51 cycloserine Mutation from literature
ethA 4326333 p.Ala381Pro missense_variant 0.56 ethionamide Uncertain significance Mutation from literature
gid 4407967 p.Leu79Ser missense_variant 0.55 streptomycin 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9138 p.Gln613Glu missense_variant 0.53 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
Rv0010c 13562 c.-4A>C upstream_gene_variant 0.5 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.62 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.54 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.53 ethionamide Uncertain significance
nusG 734637 c.384G>A synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.51 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.61 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.43 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777416 c.1065G>T synonymous_variant 0.47 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.46 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.45 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.54 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 0.52 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.47 isoniazid Not assoc w R
PPE35 2167819 p.Gly932Ser missense_variant 0.6 pyrazinamide Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.46 pyrazinamide Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.53 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.56 pyrazinamide Not assoc w R
Rv1979c 2221939 p.Arg409Gln missense_variant 0.36 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.55 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.43 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.6 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.55 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040976 c.-272T>G upstream_gene_variant 0.65 pyrazinamide
glpK 4139947 c.-192C>A upstream_gene_variant 0.69 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4238963 c.-900C>T upstream_gene_variant 0.4 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 0.57 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.61 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.36 ethambutol Not assoc w R
whiB6 4338594 c.-73T>A upstream_gene_variant 0.54 capreomycin
amikacin
kanamycin
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
whiB6 4338794 c.-273A>G upstream_gene_variant 0.51 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.53 streptomycin Not assoc w R
gid 4407714 p.Lys163Asn missense_variant 0.53 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.52 streptomycin Not assoc w R