TB-Profiler result

Run: ERR2513557
Summary

Run ID: ERR2513557

Sample name:

Date: 20-10-2023 10:57:07

Number of reads: 5456843

Percentage reads mapped: 99.29

Strain: lineage4;lineage1.1.3.3

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
lineage4 Euro-American LAM;T;S;X;H None 0.07
lineage1 Indo-Oceanic EAI RD239 0.91
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.91
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.91
lineage1.1.3.3 Indo-Oceanic NA RD239 0.89
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 0.9
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.9
gyrA 9143 c.1842T>C synonymous_variant 0.9
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 0.93
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
rpoC 763884 p.Ala172Val missense_variant 0.93
rpoC 763886 c.517C>A synonymous_variant 0.94
rpoC 765171 p.Pro601Leu missense_variant 0.89
rpoC 765230 p.Ala621Thr missense_variant 0.9
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776006 c.2475C>T synonymous_variant 0.89
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpL5 776826 p.Glu552Gly missense_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.9
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 0.92
PPE35 2167983 p.Gly877Asp missense_variant 0.89
PPE35 2168124 p.Gly830Glu missense_variant 0.89
PPE35 2169630 p.Asn328Ser missense_variant 0.86
PPE35 2169757 p.Asn286Asp missense_variant 0.89
Rv1979c 2222308 p.Asp286Gly missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.9
kasA 2519100 p.Ala329Val missense_variant 0.87
ahpC 2726051 c.-142G>A upstream_gene_variant 0.91
Rv2752c 3064632 c.1560C>T synonymous_variant 0.88
ald 3086788 c.-32T>C upstream_gene_variant 0.96
Rv3083 3448714 p.Asp71His missense_variant 0.93
Rv3083 3449709 c.1206C>G synonymous_variant 0.9
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.87
fprA 3475159 p.Asn385Asp missense_variant 0.89
alr 3840493 c.928C>T synonymous_variant 0.85
alr 3841276 p.Val49Met missense_variant 0.9
alr 3841349 c.72C>A synonymous_variant 0.89
clpC1 4040517 p.Val63Ala missense_variant 0.92
embC 4240207 c.345G>A synonymous_variant 0.84
embC 4240671 p.Thr270Ile missense_variant 0.86
embC 4241042 p.Asn394Asp missense_variant 0.89
embA 4243848 p.Val206Met missense_variant 0.92
embA 4245969 p.Pro913Ser missense_variant 0.9
embB 4247646 p.Glu378Ala missense_variant 0.88
aftB 4267431 p.Ser469Leu missense_variant 0.87
ubiA 4269387 p.Glu149Asp missense_variant 0.86
aftB 4269606 c.-770T>C upstream_gene_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.91
gid 4407588 c.615A>G synonymous_variant 0.91
gid 4407780 c.423G>A synonymous_variant 0.91
gid 4407873 c.330G>T synonymous_variant 0.94