TB-Profiler result

Run: SRR25340766
Summary

Run ID: SRR25340766

Sample name:

Date: 04-03-2024 22:48:33

Number of reads: 5707461

Percentage reads mapped: 99.29

Strain: lineage3;lineage1.1.2

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 0.49
lineage1 Indo-Oceanic EAI RD239 0.51
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.49
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.51
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 6112 p.Met291Ile missense_variant 0.44
gyrB 6124 c.885C>T synonymous_variant 0.43
gyrB 6963 p.Arg575His missense_variant 0.64
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.37
gyrA 9143 c.1842T>C synonymous_variant 0.43
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.58
rpoC 762434 c.-936T>G upstream_gene_variant 0.51
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.52
rpoC 763886 c.517C>A synonymous_variant 0.52
rpoC 765171 p.Pro601Leu missense_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776181 p.Asp767Ala missense_variant 0.48
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406503 p.Val280Leu missense_variant 0.47
embR 1417019 p.Cys110Tyr missense_variant 0.44
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154674 p.Ala480Ser missense_variant 0.43
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.47
Rv1979c 2222308 p.Asp286Gly missense_variant 0.48
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.54
kasA 2518132 c.18C>T synonymous_variant 0.55
ahpC 2726051 c.-142G>A upstream_gene_variant 0.32
ahpC 2726105 c.-88G>A upstream_gene_variant 0.63
ahpC 2726117 c.-76T>A upstream_gene_variant 0.61
Rv2752c 3064632 c.1560C>T synonymous_variant 0.55
Rv2752c 3065538 c.654G>A synonymous_variant 0.48
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.6
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.58
fprA 3475159 p.Asn385Asp missense_variant 0.55
Rv3236c 3613116 p.Val1Met missense_variant 0.43
fbiA 3640656 p.Asp38Glu missense_variant 0.63
alr 3841590 c.-170G>A upstream_gene_variant 0.56
clpC1 4040517 p.Val63Ala missense_variant 0.51
embC 4240483 c.621G>C synonymous_variant 0.49
embC 4240671 p.Thr270Ile missense_variant 0.56
embC 4241042 p.Asn394Asp missense_variant 0.59
embC 4242075 p.Arg738Gln missense_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243848 p.Val206Met missense_variant 0.54
embA 4245969 p.Pro913Ser missense_variant 0.52
embB 4247646 p.Glu378Ala missense_variant 0.59
aftB 4268156 c.681C>T synonymous_variant 0.54
aftB 4268719 p.Asn40Asp missense_variant 0.4
ubiA 4269387 p.Glu149Asp missense_variant 0.52
aftB 4269606 c.-770T>C upstream_gene_variant 0.5
whiB6 4338224 c.297delC frameshift_variant 0.61
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.49
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.46
gid 4407979 p.Pro75Leu missense_variant 0.48