TB-Profiler result

Run: SRR25827442
Summary

Run ID: SRR25827442

Sample name:

Date: 21-03-2024 07:53:34

Number of reads: 3416284

Percentage reads mapped: 49.98

Strain: lineage4.2.2;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 (0.71)
Isoniazid R fabG1 c.-15C>T (0.68), katG p.Ser315Thr (0.34)
Ethambutol R embB p.Gly406Ala (0.91)
Pyrazinamide R pncA c.-11A>G (0.64)
Streptomycin R rrs n.514A>C (0.71)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides R rrs n.1401A>G (0.69)
Amikacin R rrs n.1401A>G (0.69)
Capreomycin R rrs n.1401A>G (0.69)
Kanamycin R rrs n.1401A>G (0.69)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.68)
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 0.68
lineage4 Euro-American LAM;T;S;X;H None 0.34
lineage4.2 Euro-American H;T;LAM None 0.35
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.64
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.34
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.61
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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.71 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.71 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.69 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.68 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.34 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.64 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.91 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8365 p.Thr355Met missense_variant 0.68
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.68
mshA 575907 p.Ala187Val missense_variant 0.65
ccsA 620625 p.Ile245Met missense_variant 0.66
rpoB 762427 p.Ser874Tyr missense_variant 0.66
rpoC 763031 c.-339T>C upstream_gene_variant 0.64
rpoC 763501 p.Asp44Glu missense_variant 0.74
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.7
mmpL5 776182 p.Asp767Asn missense_variant 0.66
mmpR5 779065 c.78_88delTTTCGAGTCCA frameshift_variant 0.3
mmpS5 779615 c.-710C>G upstream_gene_variant 0.65
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.59
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475518 n.1861A>G non_coding_transcript_exon_variant 0.32
fabG1 1673188 c.-252C>A upstream_gene_variant 0.39
rpsA 1834177 c.636A>C synonymous_variant 0.55
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.67
katG 2155021 p.Ile364Thr missense_variant 0.57
PPE35 2167926 p.Leu896Ser missense_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.28
ald 3086742 c.-78A>C upstream_gene_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449738 p.His412Arg missense_variant 0.59
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.38
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.85
embB 4247028 p.Leu172Arg missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.65
gid 4407712 p.Gly164Asp missense_variant 0.32
gid 4407927 p.Glu92Asp missense_variant 0.65