TB-Profiler result

Run: SRR25340836

Summary

Run ID: SRR25340836

Sample name:

Date: 13-02-2024 00:58:30

Number of reads: 4140292

Percentage reads mapped: 99.27

Strain: lineage3;lineage1.2.2.2

Drug-resistance: Sensitive


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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 0.17
lineage1 Indo-Oceanic EAI RD239 0.82
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.8
lineage1.2.2.2 Indo-Oceanic NA RD239 0.82
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
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
gyrB 5075 c.-165C>T upstream_gene_variant 0.84
gyrB 6112 p.Met291Ile missense_variant 0.81
gyrA 7268 c.-34C>T upstream_gene_variant 0.82
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.73
gyrA 9143 c.1842T>C synonymous_variant 0.81
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575273 c.-75G>T upstream_gene_variant 0.85
rpoB 759746 c.-61C>T upstream_gene_variant 0.16
rpoC 762434 c.-936T>G upstream_gene_variant 0.24
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.77
rpoC 763886 c.517C>A synonymous_variant 0.77
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778433 c.-557G>A upstream_gene_variant 0.31
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781420 c.-140C>T upstream_gene_variant 0.16
embR 1417019 p.Cys110Tyr missense_variant 0.78
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156355 c.-244C>T upstream_gene_variant 0.74
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.82
PPE35 2169938 c.675C>T synonymous_variant 0.82
Rv1979c 2222308 p.Asp286Gly missense_variant 0.83
Rv1979c 2223051 c.114G>A synonymous_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 0.8
kasA 2518505 p.Ala131Thr missense_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 0.74
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27
pepQ 2859606 c.813G>A synonymous_variant 0.77
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.77
fprA 3473820 c.-187C>A upstream_gene_variant 0.19
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.84
fprA 3475159 p.Asn385Asp missense_variant 0.83
clpC1 4040517 p.Val63Ala missense_variant 0.78
embC 4240671 p.Thr270Ile missense_variant 0.83
embC 4241042 p.Asn394Asp missense_variant 0.88
embC 4242075 p.Arg738Gln missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243168 c.-65C>T upstream_gene_variant 0.81
embA 4245969 p.Pro913Ser missense_variant 0.89
embB 4247646 p.Glu378Ala missense_variant 0.85
ubiA 4269387 p.Glu149Asp missense_variant 0.84
aftB 4269606 c.-770T>C upstream_gene_variant 0.75
ethA 4326148 c.1326G>T synonymous_variant 0.82
ethA 4326439 p.Asn345Lys missense_variant 0.89
ethA 4328322 c.-849G>T upstream_gene_variant 0.28
whiB6 4338203 p.Arg107Cys missense_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.83
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 0.88
gid 4407873 c.330G>T synonymous_variant 0.9
gid 4408044 c.159C>T synonymous_variant 0.19