TB-Profiler result

Run: ERR7911634
Summary

Run ID: ERR7911634

Sample name:

Date: 2024-04-15T02:20:06.048304

Number of reads: 3151575

Percentage reads mapped: 99.67

Median coverage: 100.0

Strain: lineage2.2.1;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 0.13
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.08
lineage2.2 East-Asian (Beijing) RD105;RD207 0.14
lineage4.4.1 Euro-American (S-type) None 0.88
lineage4 Euro-American None 0.91
lineage4.4.1.1 Euro-American None 0.85
lineage4.4 Euro-American None 0.87
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)
p.Ser94Ala Assoc w R - Interim 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 embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gln10Pro Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Tyr Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ser91Pro Assoc w R
p.Asp94Tyr Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ser94Ala Assoc w R - Interim
ethA c.65delA Assoc w R
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 7572 p.Ser91Pro missense_variant 0.23 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
gyrA 7581 p.Asp94Tyr missense_variant 0.79 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.14 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
inhA 1674481 p.Ser94Ala missense_variant 0.91 isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R - Interim
katG 2155168 p.Ser315Thr missense_variant 0.89 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Pro missense_variant 0.85 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.81 kanamycin Assoc w R
embB 4247429 p.Met306Val missense_variant 0.13 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.91 ethambutol Assoc w R
ethA 4327408 c.65delA frameshift_variant 0.21 ethionamide Assoc w R
ethR 4327831 p.Ala95Thr missense_variant 0.16 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
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 8164 p.Ala288Asp missense_variant 0.14 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9138 p.Gln613Glu missense_variant 0.82 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 0.19 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.15 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.15 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 763555 c.186C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764931 p.Ala521Asp missense_variant 0.14 rifampicin Uncertain significance
rpoC 764936 p.Gln523Glu missense_variant 0.85 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 0.18 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.12 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 777416 c.1065G>T synonymous_variant 0.87 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mmpS5 778979 c.-74G>T upstream_gene_variant 0.14 clofazimine Uncertain significance
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.14 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
rrl 1475954 n.2297A>C non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rpsA 1833585 p.Asp15Gly missense_variant 0.84 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.12 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 0.85 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.14 pyrazinamide Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.84 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.88 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3065039 p.Tyr385Asp missense_variant 0.79 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.9 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.79 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.84 pyrazinamide Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.88 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 0.12 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.25 ethambutol Not assoc w R
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
gid 4407588 c.615A>G synonymous_variant 0.18 streptomycin Not assoc w R
gid 4407790 p.Ala138Glu missense_variant 0.83 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.18 streptomycin Not assoc w R