TB-Profiler result

Run: SRR5266542
Summary

Run ID: SRR5266542

Sample name:

Date: 2024-04-16T11:12:01.825285

Number of reads: 978340

Percentage reads mapped: 94.78

Median coverage: 35.0

Strain: lineage2.2.1

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 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 0.99
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA c.449dupG Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide ethA c.110delA Assoc w R
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 7582 p.Asp94Ala missense_variant 1.0 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)
rpoB 761155 p.Ser450Leu missense_variant 0.81 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 amikacin Assoc w R
kanamycin Assoc w R
capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288792 c.449dupG frameshift_variant 1.0 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol Assoc w R
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide Assoc w R
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 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.96 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.94 ethionamide Uncertain significance
rpoB 760715 c.909C>G synonymous_variant 0.18 rifampicin
rpoB 760718 c.912C>T synonymous_variant 0.2 rifampicin
rpoB 760724 c.918T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760730 c.924T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760751 c.945G>C synonymous_variant 0.17 rifampicin
rpoB 760757 c.951T>C synonymous_variant 0.16 rifampicin
rpoB 760759 p.Val318Ala missense_variant 0.16 rifampicin
rpoB 760769 c.963C>G synonymous_variant 0.15 rifampicin
rpoB 760775 c.969G>C synonymous_variant 0.15 rifampicin
rpoB 760776 c.970_972delTCGinsAGC synonymous_variant 0.15 rifampicin
rpoB 760793 c.987A>G synonymous_variant 0.15 rifampicin
rpoB 761015 c.1209G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.15 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761102 c.1296A>G synonymous_variant 0.18 rifampicin
rpoB 761150 c.1344A>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761153 c.1347G>C synonymous_variant 0.2 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761207 c.1401C>T synonymous_variant 0.15 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.16 rifampicin
rpoB 761219 c.1413G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 762929 c.3123G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 763594 c.225C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764703 p.Lys445Arg missense_variant 1.0 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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800720 c.-89T>C upstream_gene_variant 0.13 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.14 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.16 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
ndh 2102409 c.633dupG frameshift_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086731 c.-89A>G upstream_gene_variant 1.0 cycloserine
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 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878141 p.Met123Leu missense_variant 0.19 rifampicin Uncertain significance
rpoA 3878143 p.Gly122Asp missense_variant 0.18 rifampicin Uncertain significance
rpoA 3878157 c.351C>G synonymous_variant 0.18 rifampicin
rpoA 3878163 c.345C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878169 c.339G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
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 4338371 p.Thr51Pro missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
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 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R