TB-Profiler result

Run: SRR25827530

Summary

Run ID: SRR25827530

Sample name:

Date: 02-02-2024 09:13:12

Number of reads: 18676137

Percentage reads mapped: 99.14

Strain: lineage4;lineage2.2.1

Drug-resistance: XDR-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 (1.00)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol R embB p.Met306Val (0.46), embB p.Gly406Ser (0.39), embB p.Gln853Pro (0.41)
Pyrazinamide R pncA p.Asp63Ala (0.37), pncA c.-11A>G (0.36)
Streptomycin R rpsL p.Lys43Arg (0.99)
Fluoroquinolones R gyrA p.Ala90Val (0.46), gyrA p.Asp94Tyr (0.40)
Moxifloxacin R gyrA p.Ala90Val (0.46), gyrA p.Asp94Tyr (0.40)
Ofloxacin R gyrA p.Ala90Val (0.46), gyrA p.Asp94Tyr (0.40)
Levofloxacin R gyrA p.Ala90Val (0.46), gyrA p.Asp94Tyr (0.40)
Ciprofloxacin R gyrA p.Ala90Val (0.46), gyrA p.Asp94Tyr (0.40)
Aminoglycosides R rrs n.1401A>G (0.29)
Amikacin R rrs n.1401A>G (0.29)
Capreomycin R rrs n.1401A>G (0.29)
Kanamycin R rrs n.1401A>G (0.29)
Cycloserine
Ethionamide R ethA c.1047dupT (0.38), ethA c.1047dupT (0.38)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.36)
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.39)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.93
lineage4 Euro-American LAM;T;S;X;H None 0.06
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.92
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.93
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
gyrA 7570 p.Ala90Val missense_variant 0.46 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Tyr missense_variant 0.4 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.39 linezolid
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.29 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289054 p.Asp63Ala missense_variant 0.37 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.36 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.36 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.46 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.39 ethambutol
embB 4249071 p.Gln853Pro missense_variant 0.41 ethambutol
ethA 4326426 c.1047dupT frameshift_variant 0.38 ethionamide, 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
gyrA 7283 c.-19G>T upstream_gene_variant 0.43
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.48
fgd1 491742 c.960T>C synonymous_variant 0.95
mshA 575907 p.Ala187Val missense_variant 0.93
ccsA 620625 p.Ile245Met missense_variant 0.93
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 764666 p.Gly433Ser missense_variant 0.8
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpL5 776182 p.Asp767Asn missense_variant 0.92
mmpS5 779615 c.-710C>G upstream_gene_variant 0.93
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.95
PPE35 2167926 p.Leu896Ser missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860365 c.54G>T synonymous_variant 0.41
Rv2752c 3066004 p.Asp63Ala missense_variant 0.34
thyA 3074069 p.Val135Phe missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.19
Rv3236c 3612813 p.Thr102Ala missense_variant 0.94
embC 4241022 p.Ala387Val missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.37
embA 4243460 c.228C>T synonymous_variant 0.91
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4249757 p.Thr1082Ala missense_variant 0.47
aftB 4267647 p.Asp397Gly missense_variant 0.93
ubiA 4269311 p.Trp175Gly missense_variant 0.39
ethA 4326900 p.Pro192Thr missense_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.93
gid 4407620 p.Tyr195His missense_variant 0.46
gid 4407927 p.Glu92Asp missense_variant 0.93