TB-Profiler result

Run: ERR9786506
Summary

Run ID: ERR9786506

Sample name:

Date: 2024-10-04T03:57:38.137691

Number of reads: 4929363

Percentage reads mapped: 99.55

Median coverage: 211.0

Strain: lineage2.2.1;lineage4.1.2.1;lineage4.7

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.33
lineage4.1 Euro-American None 0.56
lineage4.1.2 Euro-American None 0.24
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.25
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.34
lineage2.2 East-Asian (Beijing) RD105;RD207 0.34
lineage4.7 Euro-American (mainly T) None 0.1
lineage4 Euro-American None 0.68
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
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 673 p.Ala225Thr missense_variant 0.3 isoniazid Uncertain significance
gyrB 6507 p.Ala423Val missense_variant 0.33 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7595 c.294C>G synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9656 c.2355C>G synonymous_variant 0.31 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
fgd1 491591 p.Lys270Met missense_variant 0.21 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.41 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.2 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.3 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.4 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.42 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.45 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.23 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.41 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.59 rifampicin Not assoc w R
rpoC 765187 c.1818C>T synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 766012 c.2643C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
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 0.39 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 0.33 streptomycin Uncertain significance
rplC 800941 p.Asp45Tyr missense_variant 0.33 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.34 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417932 c.-585G>C upstream_gene_variant 0.24 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472076 n.231G>T non_coding_transcript_exon_variant 0.32 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.1 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.41 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.9 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 0.28 isoniazid Not assoc w R
katG 2155824 c.288C>T synonymous_variant 0.31 isoniazid Not assoc w R - Interim
katG 2156007 c.105C>T synonymous_variant 0.4 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.29 pyrazinamide Not assoc w R
PPE35 2168448 p.Gln722Arg missense_variant 0.34 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223421 c.-257G>A upstream_gene_variant 0.34 bedaquiline
clofazimine
kasA 2518076 c.-39C>T upstream_gene_variant 0.16 isoniazid
Rv2477c 2784387 c.-347_-346dupTA upstream_gene_variant 0.29 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2752c 3064764 c.1428C>T synonymous_variant 0.36 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.97 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.34 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.36 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.96 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.32 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627293 c.57G>A synonymous_variant 0.33 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
glpK 4139183 c.572dupG frameshift_variant 0.22 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.28 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.56 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.29 ethambutol Not assoc w R
embA 4244262 c.1030C>T synonymous_variant 0.37 ethambutol Not assoc w R - Interim
embB 4249732 c.3219C>G synonymous_variant 0.26 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.3 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.31 ethionamide Uncertain significance
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 0.93 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.37 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.33 streptomycin Not assoc w R