TB-Profiler result

Run: SRR15600376
Summary

Run ID: SRR15600376

Sample name:

Date: 2024-10-04T09:45:18.136447

Number of reads: 8422593

Percentage reads mapped: 92.11

Median coverage: 254.0

Strain: lineage2.2.1.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 0.99
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 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 katG p.Asn138Ser Uncertain significance Mutation from literature
ethambutol
pyrazinamide
streptomycin rrs n.462C>T 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
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
gyrA 7570 p.Ala90Val missense_variant 0.96 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance Mutation from literature
katG 2155699 p.Asn138Ser missense_variant 0.98 isoniazid 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 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
mshA 576108 p.Ala254Gly missense_variant 0.23 isoniazid
ethionamide
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 0.98 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.98 ethionamide Uncertain significance
rpoB 763028 c.3222T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764353 c.984G>C synonymous_variant 0.17 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765753 p.Asp795Ala missense_variant 0.13 rifampicin Uncertain significance
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
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475436 n.1779C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476105 n.2448_2449delGAinsT non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833940 c.399C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 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
katG 2154469 p.Gly548Ala missense_variant 1.0 isoniazid
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
eis 2714846 p.Val163Ile missense_variant 1.0 kanamycin Not assoc w R
amikacin Not assoc w R
Rv2477c 2783929 c.114C>G synonymous_variant 0.22 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
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
mtrB 3626930 c.-317A>G upstream_gene_variant 0.13 rifampicin
bedaquiline
mtrB 3626972 c.-359A>G upstream_gene_variant 0.17 rifampicin
bedaquiline
mtrB 3626987 c.-374C>G upstream_gene_variant 0.14 rifampicin
bedaquiline
rpoA 3877818 c.690A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878364 c.144A>T synonymous_variant 0.14 rifampicin
rpoA 3878367 c.141C>G synonymous_variant 0.14 rifampicin
rpoA 3878742 c.-235G>A upstream_gene_variant 0.13 rifampicin
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
embA 4245131 c.1899G>A synonymous_variant 0.94 ethambutol Not assoc w R - Interim
embB 4248115 c.1602C>T synonymous_variant 0.9 ethambutol Not assoc w R
embB 4248304 c.1791G>C synonymous_variant 0.15 ethambutol
embB 4248316 c.1803C>G synonymous_variant 0.15 ethambutol
embB 4248319 c.1806A>G synonymous_variant 0.17 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.99 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