TB-Profiler result

Run: SRR25827481
Summary

Run ID: SRR25827481

Sample name:

Date: 02-02-2024 04:53:18

Number of reads: 10448796

Percentage reads mapped: 98.93

Strain: lineage3;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 (0.73), katG p.Ser315Thr (0.75)
Ethambutol R embA c.-16C>T (0.64), embB p.Gln497Arg (0.77)
Pyrazinamide R pncA p.Gly132Ala (0.73)
Streptomycin R rpsL p.Lys43Arg (0.73), gid c.102delG (0.30)
Fluoroquinolones R gyrA p.Asp94Gly (0.76)
Moxifloxacin R gyrA p.Asp94Gly (0.76)
Ofloxacin R gyrA p.Asp94Gly (0.76)
Levofloxacin R gyrA p.Asp94Gly (0.76)
Ciprofloxacin R gyrA p.Asp94Gly (0.76)
Aminoglycosides R rrs n.1401A>G (0.73)
Amikacin R rrs n.1401A>G (0.73)
Capreomycin R rrs n.1401A>G (0.73)
Kanamycin R rrs n.1401A>G (0.73)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.73)
Clofazimine
Para-aminosalicylic_acid
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 0.25
lineage2 East-Asian Beijing RD105 0.76
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.75
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.75
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 0.76 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.82 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.73 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.73 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.73 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.75 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.73 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.64 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.77 ethambutol
gid 4408100 c.102delG frameshift_variant 0.3 streptomycin
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 8131 p.Gln277Arg missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.77
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.81
ccsA 620625 p.Ile245Met missense_variant 0.79
rpoB 759746 c.-61C>T upstream_gene_variant 0.27
rpoC 762434 c.-936T>G upstream_gene_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 0.8
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.74
mmpR5 779326 p.Glu113Lys missense_variant 0.69
mmpS5 779615 c.-710C>G upstream_gene_variant 0.77
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.72
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156344 c.-233C>G upstream_gene_variant 0.26
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 0.24
pncA 2289365 c.-125delC upstream_gene_variant 0.23
ahpC 2726105 c.-88G>A upstream_gene_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474773 p.Ala256Gly missense_variant 0.24
whiB7 3568425 c.255T>G synonymous_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 0.72
clpC1 4040753 c.-49G>A upstream_gene_variant 0.19
embC 4241022 p.Ala387Val missense_variant 0.75
embC 4242075 p.Arg738Gln missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.74
embA 4245835 p.Leu868Arg missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.68
aftB 4268753 c.84T>G synonymous_variant 0.77
whiB6 4338595 c.-75delG upstream_gene_variant 0.3
whiB6 4338599 c.-79_-78delTAinsC upstream_gene_variant 0.7
whiB6 4338602 c.-81A>T upstream_gene_variant 0.66
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.76
gid 4407927 p.Glu92Asp missense_variant 0.73