TB-Profiler result

Run: SRR5341451

Summary

Run ID: SRR5341451

Sample name:

Date: 20-10-2023 18:50:00

Number of reads: 5472221

Percentage reads mapped: 98.16

Strain: lineage3;lineage1.1.2

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.18)
Ethambutol
Pyrazinamide
Streptomycin R rrs n.517C>T (0.26), gid c.351delG (0.77)
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 0.18
lineage1 Indo-Oceanic EAI RD239 0.82
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.84
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.84
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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.26 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid
gid 4407851 c.351delG frameshift_variant 0.77 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
gyrB 6112 p.Met291Ile missense_variant 0.78
gyrB 6124 c.885C>T synonymous_variant 0.77
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.83
gyrA 9143 c.1842T>C synonymous_variant 0.72
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 0.18
rpoB 760490 c.684C>T synonymous_variant 0.82
rpoC 762371 c.-999G>A upstream_gene_variant 0.78
rpoC 762434 c.-936T>G upstream_gene_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.9
rpoC 763886 c.517C>A synonymous_variant 0.9
rpoC 765171 p.Pro601Leu missense_variant 0.83
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.81
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416631 c.717C>A synonymous_variant 0.23
embR 1417019 p.Cys110Tyr missense_variant 0.8
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.86
Rv1979c 2222308 p.Asp286Gly missense_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.16
pncA 2289365 c.-125delC upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 0.79
eis 2715016 p.Arg106His missense_variant 0.83
ahpC 2726051 c.-142G>A upstream_gene_variant 0.86
pepQ 2860398 c.21A>C synonymous_variant 0.84
Rv2752c 3064632 c.1560C>T synonymous_variant 0.88
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.79
Rv3083 3448714 p.Asp71His missense_variant 0.85
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.81
fprA 3475159 p.Asn385Asp missense_variant 0.89
alr 3841473 c.-53G>A upstream_gene_variant 0.15
clpC1 4038338 c.2364_2366dupGAT disruptive_inframe_insertion 0.76
clpC1 4040517 p.Val63Ala missense_variant 0.9
embC 4240671 p.Thr270Ile missense_variant 0.85
embC 4241042 p.Asn394Asp missense_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.77
embA 4245969 p.Pro913Ser missense_variant 0.82
embB 4247646 p.Glu378Ala missense_variant 0.84
ubiA 4269387 p.Glu149Asp missense_variant 0.81
aftB 4269606 c.-770T>C upstream_gene_variant 0.83
ethA 4326983 p.Pro164Leu missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.81
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.76