TB-Profiler result

Run: SRR25827306
Summary

Run ID: SRR25827306

Sample name:

Date: 31-01-2024 22:42:39

Number of reads: 7391170

Percentage reads mapped: 98.86

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 (0.68)
Isoniazid R katG p.Ser315Thr (0.74)
Ethambutol R embB p.Met306Val (0.60)
Pyrazinamide R pncA p.Thr177Pro (0.36)
Streptomycin R rpsL p.Lys43Arg (0.63), gid c.102delG (0.32)
Fluoroquinolones R gyrA p.Ala90Val (0.35), gyrA p.Asp94Ala (0.50)
Moxifloxacin R gyrA p.Ala90Val (0.35), gyrA p.Asp94Ala (0.50)
Ofloxacin R gyrA p.Ala90Val (0.35), gyrA p.Asp94Ala (0.50)
Levofloxacin R gyrA p.Ala90Val (0.35), gyrA p.Asp94Ala (0.50)
Ciprofloxacin R gyrA p.Ala90Val (0.35), gyrA p.Asp94Ala (0.50)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.44)
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 0.33
lineage2 East-Asian Beijing RD105 0.65
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.64
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.63
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 0.35 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.5 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.63 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.74 isoniazid
pncA 2288713 p.Thr177Pro missense_variant 0.36 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.44 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.6 ethambutol
gid 4408100 c.102delG frameshift_variant 0.32 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 575907 p.Ala187Val missense_variant 0.63
ccsA 620553 c.663T>C synonymous_variant 0.23
ccsA 620625 p.Ile245Met missense_variant 0.65
rpoB 759746 c.-61C>T upstream_gene_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 0.3
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 764817 p.Val483Ala missense_variant 0.25
rpoC 764840 p.Ile491Val missense_variant 0.34
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.96
mmpL5 776182 p.Asp767Asn missense_variant 0.62
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.66
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.6
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.33
pncA 2289365 c.-125delC upstream_gene_variant 0.35
ahpC 2726105 c.-88G>A upstream_gene_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.69
fbiB 3642627 p.Arg365Gly missense_variant 0.36
alr 3841473 c.-53G>A upstream_gene_variant 0.33
clpC1 4039180 p.Arg509Gly missense_variant 0.3
embC 4240861 c.999G>A synonymous_variant 0.23
embC 4241022 p.Ala387Val missense_variant 0.34
embC 4242075 p.Arg738Gln missense_variant 0.31
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 0.19
embB 4248554 p.Gly681Ser missense_variant 0.3
embB 4249757 p.Thr1082Ala missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 0.69
ubiA 4269296 p.Met180Val missense_variant 0.34
whiB6 4338365 p.Cys53Gly missense_variant 0.38
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.96
gid 4407620 p.Tyr195His missense_variant 0.32
gid 4407927 p.Glu92Asp missense_variant 0.63