TB-Profiler result

Run: SRR29096399
Summary

Run ID: SRR29096399

Sample name:

Date: 2024-10-04T02:52:49.961021

Number of reads: 983186

Percentage reads mapped: 98.24

Median coverage: 31.0

Strain: lineage2.2.1

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 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
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
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 8915 c.1614A>G synonymous_variant 0.26 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8918 c.1617C>G synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 8924 c.1623C>T synonymous_variant 0.31 levofloxacin
moxifloxacin
gyrA 8933 c.1632G>A synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8939 c.1638T>C synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 8942 c.1641G>C synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 8945 c.1644G>T synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 8946 c.1645_1647delTTGinsCTC synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8987 c.1686C>G synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 8990 c.1689C>T synonymous_variant 0.27 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8993 c.1692C>T synonymous_variant 0.28 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8996 c.1695T>C synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 8998 p.Leu566Trp missense_variant 0.28 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9023 c.1722A>C synonymous_variant 0.26 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9029 c.1728T>G synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 9032 c.1731T>C synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 9035 c.1734G>A synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.93 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 1.0 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 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 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674628 p.Ser143Ala missense_variant 0.17 isoniazid
ethionamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834330 c.789C>G synonymous_variant 0.31 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.3 pyrazinamide Not assoc w R - Interim
rpsA 1834361 c.820T>C synonymous_variant 0.3 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>C synonymous_variant 0.29 pyrazinamide
rpsA 1834408 c.867C>T synonymous_variant 0.32 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.31 pyrazinamide
rpsA 1834423 c.882G>T synonymous_variant 0.28 pyrazinamide
rpsA 1834432 c.891G>C synonymous_variant 0.29 pyrazinamide
rpsA 1834732 c.1191T>C synonymous_variant 0.25 pyrazinamide
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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4039883 c.822G>A synonymous_variant 0.19 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.24 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.19 pyrazinamide
clpC1 4039925 c.780C>T synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039931 c.774T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039934 c.771G>C synonymous_variant 0.15 pyrazinamide
embC 4241125 c.1263G>A synonymous_variant 0.17 ethambutol
embC 4241135 p.Val425Leu missense_variant 0.18 ethambutol
embC 4241140 c.1278A>G synonymous_variant 0.18 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 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 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R