TB-Profiler result

Run: SRR14801415
Summary

Run ID: SRR14801415

Sample name:

Date: 2024-10-04T00:32:22.058798

Number of reads: 1551764

Percentage reads mapped: 95.07

Median coverage: 47.0

Strain: lineage2.2.1;lineage4.8

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 0.3
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.26
lineage2.2 East-Asian (Beijing) RD105;RD207 0.28
lineage4 Euro-American None 0.75
lineage4.8 Euro-American (mainly T) RD219 0.75
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 0.36 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.31 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.3 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.27 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.75 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.31 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.26 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.7 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.35 rifampicin Not assoc w R
rpoC 763528 c.159G>A synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765753 p.Asp795Ala missense_variant 0.12 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.35 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.19 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781892 c.333A>G synonymous_variant 0.15 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.15 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.16 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.33 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 0.25 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.69 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.26 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.3 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.84 pyrazinamide Not assoc w R
PPE35 2168247 p.Leu789Arg missense_variant 0.85 pyrazinamide Uncertain significance
PPE35 2170623 c.-11G>A upstream_gene_variant 0.21 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289952 c.-711C>G upstream_gene_variant 0.69 pyrazinamide
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.7 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.27 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.26 pyrazinamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.67 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.33 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878783 c.-276C>T upstream_gene_variant 0.74 rifampicin Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.74 pyrazinamide 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 0.21 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 0.27 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.31 streptomycin Not assoc w R