TB-Profiler result

Run: SRR25827778
Summary

Run ID: SRR25827778

Sample name:

Date: 16-03-2024 07:22:04

Number of reads: 2561106

Percentage reads mapped: 96.41

Strain: lineage2.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.99)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.40), embB p.Gly406Asp (0.62)
Pyrazinamide R pncA p.Leu27Pro (0.29)
Streptomycin R rpsL p.Lys43Arg (0.38), rpsL p.Lys88Met (0.71)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin R eis c.-14C>T (0.59)
Capreomycin
Kanamycin R eis c.-14C>T (0.59)
Cycloserine
Ethionamide R ethA p.Trp240* (0.65)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.61)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.38 streptomycin
rpsL 781822 p.Lys88Met missense_variant 0.71 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.61 linezolid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.29 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.59 kanamycin, amikacin
embB 4247429 p.Met306Val missense_variant 0.4 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.62 ethambutol
ethA 4326754 p.Trp240* stop_gained 0.65 ethionamide
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
gyrB 5078 c.-162_-161insG upstream_gene_variant 0.31
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Ser missense_variant 0.3
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.65
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 0.38
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.72
mmpR5 779199 c.211delG frameshift_variant 0.65
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673784 c.-418G>T upstream_gene_variant 0.17
inhA 1673787 c.-415G>C upstream_gene_variant 0.18
inhA 1673799 c.-403T>C upstream_gene_variant 0.19
inhA 1673802 c.-400A>G upstream_gene_variant 0.18
inhA 1673808 c.-394A>C upstream_gene_variant 0.18
fabG1 1673829 p.Asn130Lys missense_variant 0.18
fabG1 1673830 p.Lys131Arg missense_variant 0.18
inhA 1673838 c.-364T>C upstream_gene_variant 0.19
inhA 1673841 c.-361A>G upstream_gene_variant 0.19
fabG1 1673844 p.Met135Ile missense_variant 0.18
inhA 1673847 c.-355A>C upstream_gene_variant 0.19
inhA 1673853 c.-349A>C upstream_gene_variant 0.19
inhA 1673856 c.-346T>C upstream_gene_variant 0.18
inhA 1673859 c.-343G>C upstream_gene_variant 0.19
inhA 1673865 c.-337C>G upstream_gene_variant 0.19
fabG1 1673870 p.Ser144Met missense_variant 0.2
inhA 1673877 c.-325C>G upstream_gene_variant 0.2
fabG1 1673905 p.Ser156Ala missense_variant 0.19
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170018 p.Ala199Ser missense_variant 0.68
Rv1979c 2221889 p.Val426Ile missense_variant 0.73
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 0.76
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3877969 p.Ala180Val missense_variant 0.76
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
embA 4246085 p.Glu951Asp missense_variant 0.65
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 0.43
whiB6 4338233 p.Ser97Pro missense_variant 0.72
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0