TB-Profiler result

Run: SRR25827711

Summary

Run ID: SRR25827711

Sample name:

Date: 02-02-2024 16:10:40

Number of reads: 7028602

Percentage reads mapped: 99.19

Strain: lineage3;lineage2.2.1.1

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.Asp435Val (0.28), rpoB p.Ser450Leu (0.62)
Isoniazid R fabG1 c.-15C>T (0.44), katG p.Ser315Thr (0.97)
Ethambutol R embB p.Met306Val (0.43), embB p.Gln497Arg (0.45)
Pyrazinamide R pncA p.Gly132Ala (0.45)
Streptomycin R rpsL p.Lys43Arg (0.87)
Fluoroquinolones R gyrA p.Ala90Val (0.39), gyrA p.Asp94Gly (0.52)
Moxifloxacin R gyrA p.Ala90Val (0.39), gyrA p.Asp94Gly (0.52)
Ofloxacin R gyrA p.Ala90Val (0.39), gyrA p.Asp94Gly (0.52)
Levofloxacin R gyrA p.Ala90Val (0.39), gyrA p.Asp94Gly (0.52)
Ciprofloxacin R gyrA p.Ala90Val (0.39), gyrA p.Asp94Gly (0.52)
Aminoglycosides R rrs n.1401A>G (0.50)
Amikacin R rrs n.1401A>G (0.50)
Capreomycin R rrs n.1401A>G (0.50)
Kanamycin R rrs n.1401A>G (0.50)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.44)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.37)
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.12
lineage2 East-Asian Beijing RD105 0.85
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.86
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.84
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.29
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 0.39 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.52 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.28 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.62 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.87 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.5 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.44 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.45 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.37 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.43 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.45 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.39
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.79
ccsA 620625 p.Ile245Met missense_variant 0.87
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 0.41
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.81
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.85
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.83
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.18
pncA 2289365 c.-125delC upstream_gene_variant 0.21
eis 2714846 p.Val163Ile missense_variant 0.31
thyA 3073987 p.Gln162Pro missense_variant 0.44
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087647 c.830dupG frameshift_variant 0.42
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 0.86
alr 3841540 c.-120T>C upstream_gene_variant 0.5
embC 4241022 p.Ala387Val missense_variant 0.46
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.84
embB 4247028 p.Leu172Arg missense_variant 0.13
embB 4247880 p.Val456Ala missense_variant 0.23
embB 4248115 c.1602C>T synonymous_variant 0.32
aftB 4267647 p.Asp397Gly missense_variant 0.88
aftB 4268753 c.84T>G synonymous_variant 0.46
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.46
gid 4407927 p.Glu92Asp missense_variant 0.87