TB-Profiler result

Run: SRR25827417

Summary

Run ID: SRR25827417

Sample name:

Date: 02-02-2024 02:21:11

Number of reads: 7925688

Percentage reads mapped: 99.18

Strain: lineage4.9;lineage2.2.1

Drug-resistance: Pre-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 (0.82)
Isoniazid R fabG1 c.-15C>T (0.23), katG p.Ser315Thr (0.82)
Ethambutol R embB p.Met306Val (0.45), embB p.Gln497Arg (0.15)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.70)
Fluoroquinolones R gyrA p.Ala90Val (0.14), gyrA p.Asp94Gly (0.63)
Moxifloxacin R gyrA p.Ala90Val (0.14), gyrA p.Asp94Gly (0.63)
Ofloxacin R gyrA p.Ala90Val (0.14), gyrA p.Asp94Gly (0.63)
Levofloxacin R gyrA p.Ala90Val (0.14), gyrA p.Asp94Gly (0.63)
Ciprofloxacin R gyrA p.Ala90Val (0.14), gyrA p.Asp94Gly (0.63)
Aminoglycosides R rrs n.1401A>G (0.21)
Amikacin R rrs n.1401A>G (0.21)
Capreomycin R rrs n.1401A>G (0.21)
Kanamycin R rrs n.1401A>G (0.21)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.23)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.72
lineage4 Euro-American LAM;T;S;X;H None 0.2
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.7
lineage4.9 Euro-American (H37Rv-like) T1 None 0.14
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.7
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 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.63 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.82 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.7 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.21 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.23 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.82 isoniazid
embB 4247429 p.Met306Val missense_variant 0.45 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.15 ethambutol
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 7362 p.Glu21Gln missense_variant 0.85
gyrA 7585 p.Ser95Thr missense_variant 0.85
gyrA 9304 p.Gly668Asp missense_variant 0.88
fgd1 491290 p.Val170Met missense_variant 0.16
fgd1 491742 c.960T>C synonymous_variant 0.8
mshA 575907 p.Ala187Val missense_variant 0.75
ccsA 620553 c.663T>C synonymous_variant 0.47
ccsA 620625 p.Ile245Met missense_variant 0.77
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
rpoC 764817 p.Val483Ala missense_variant 0.57
rpoC 764840 p.Ile491Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 0.89
mmpL5 776100 p.Thr794Ile missense_variant 0.79
mmpL5 776182 p.Asp767Asn missense_variant 0.71
mmpS5 779615 c.-710C>G upstream_gene_variant 0.71
rpsL 781395 c.-165T>C upstream_gene_variant 0.83
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7
rrs 1471659 n.-187C>T upstream_gene_variant 0.96
rpsA 1834177 c.636A>C synonymous_variant 0.74
tlyA 1917972 c.33A>G synonymous_variant 0.83
katG 2154724 p.Arg463Leu missense_variant 0.75
PPE35 2167926 p.Leu896Ser missense_variant 0.76
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.89
ald 3086788 c.-32T>C upstream_gene_variant 0.85
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.86
whiB7 3568425 c.255T>G synonymous_variant 0.21
Rv3236c 3612813 p.Thr102Ala missense_variant 0.7
embC 4241022 p.Ala387Val missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 0.85
embA 4243460 c.228C>T synonymous_variant 0.75
embB 4247028 p.Leu172Arg missense_variant 0.2
embB 4249757 p.Thr1082Ala missense_variant 0.41
aftB 4267647 p.Asp397Gly missense_variant 0.72
whiB6 4338595 c.-75delG upstream_gene_variant 0.86
gid 4407588 c.615A>G synonymous_variant 0.84
gid 4407620 p.Tyr195His missense_variant 0.18
gid 4407927 p.Glu92Asp missense_variant 0.77