TB-Profiler result

Run: SRR25827720

Summary

Run ID: SRR25827720

Sample name:

Date: 02-02-2024 16:16:39

Number of reads: 5867974

Percentage reads mapped: 98.88

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 (1.00)
Isoniazid R fabG1 c.-15C>T (0.60), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-11C>A (0.20), embB p.Met306Val (0.27), embB p.Gln497Arg (0.73)
Pyrazinamide R pncA p.Gly132Ala (0.41), pncA p.Leu27Pro (0.21)
Streptomycin R rpsL p.Lys43Arg (0.81), rpsL p.Lys88Arg (0.17)
Fluoroquinolones R gyrA p.Ala90Val (0.43), gyrA p.Ser91Pro (0.43)
Moxifloxacin R gyrA p.Ala90Val (0.43), gyrA p.Ser91Pro (0.43)
Ofloxacin R gyrA p.Ala90Val (0.43), gyrA p.Ser91Pro (0.43)
Levofloxacin R gyrA p.Ala90Val (0.43), gyrA p.Ser91Pro (0.43)
Ciprofloxacin R gyrA p.Ala90Val (0.43), gyrA p.Ser91Pro (0.43)
Aminoglycosides R rrs n.1401A>G (0.14)
Amikacin R rrs n.1401A>G (0.14)
Capreomycin R rrs n.1401A>G (0.14)
Kanamycin R rrs n.1401A>G (0.14)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.60), ethA p.Ser57Tyr (0.16)
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 0.2
lineage2 East-Asian Beijing RD105 0.81
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.8
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.77
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 0.43 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.43 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.81 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.17 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.6 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.41 pyrazinamide
pncA 2289162 p.Leu27Pro missense_variant 0.21 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.2 ethambutol
embB 4247429 p.Met306Val missense_variant 0.27 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.73 ethambutol
ethA 4327304 p.Ser57Tyr missense_variant 0.16 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Thr missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.56
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.55
ccsA 620625 p.Ile245Met missense_variant 0.8
rpoB 759746 c.-61C>T upstream_gene_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764533 c.1164C>A synonymous_variant 0.23
rpoC 764840 p.Ile491Val missense_variant 0.59
rpoC 766488 p.Pro1040Arg missense_variant 0.2
rpoC 767123 p.Val1252Leu missense_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.57
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.79
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.76
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 2289365 c.-125delC upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 0.19
Rv2752c 3064700 p.Ser498Pro missense_variant 0.35
Rv2752c 3065864 p.Ala110Ser missense_variant 0.41
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473820 c.-187C>A upstream_gene_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.16
whiB7 3568555 p.Leu42Pro missense_variant 0.24
whiB7 3568854 c.-176delG upstream_gene_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 0.82
embC 4241022 p.Ala387Val missense_variant 0.57
embC 4242075 p.Arg738Gln missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.71
embB 4247028 p.Leu172Arg missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 0.72
ethA 4326593 p.Cys294Phe missense_variant 0.34
ethA 4326676 p.Ser266Arg missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.59
gid 4407927 p.Glu92Asp missense_variant 0.76