TB-Profiler result

Run: ERR2513014
Summary

Run ID: ERR2513014

Sample name:

Date: 20-10-2023 10:13:13

Number of reads: 3968798

Percentage reads mapped: 99.52

Strain: lineage4.1.2.1;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
lineage4 Euro-American LAM;T;S;X;H None 0.77
lineage1 Indo-Oceanic EAI RD239 0.22
lineage4.1 Euro-American T;X;H None 0.76
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.23
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.21
lineage4.1.2 Euro-American T;H None 0.78
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.8
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 0.23
gyrB 6124 c.885C>T synonymous_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.24
gyrA 9143 c.1842T>C synonymous_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.74
fgd1 491742 c.960T>C synonymous_variant 0.19
mshA 575679 p.Asn111Ser missense_variant 0.74
rpoB 760115 c.309C>T synonymous_variant 0.78
rpoC 763031 c.-339T>C upstream_gene_variant 0.25
rpoC 763884 p.Ala172Val missense_variant 0.22
rpoC 763886 c.517C>A synonymous_variant 0.22
rpoC 765150 p.Gly594Glu missense_variant 0.75
rpoC 765171 p.Pro601Leu missense_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.23
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673283 c.-157A>C upstream_gene_variant 0.2
tlyA 1917777 c.-163A>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.19
katG 2155557 c.555C>T synonymous_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 0.2
PPE35 2167983 p.Gly877Asp missense_variant 0.2
PPE35 2168963 c.1650A>G synonymous_variant 0.22
PPE35 2169421 p.Asn398Tyr missense_variant 0.77
Rv1979c 2221783 p.Ala461Glu missense_variant 0.24
Rv1979c 2222308 p.Asp286Gly missense_variant 0.24
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288924 p.Phe106Leu missense_variant 0.24
kasA 2518076 c.-39C>T upstream_gene_variant 0.81
kasA 2518132 c.18C>T synonymous_variant 0.19
kasA 2519096 p.Val328Ile missense_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 0.23
ahpC 2726672 c.480G>A synonymous_variant 0.25
Rv2752c 3064632 c.1560C>T synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 0.99
Rv3083 3448714 p.Asp71His missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.23
fprA 3475159 p.Asn385Asp missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 0.23
embC 4240671 p.Thr270Ile missense_variant 0.19
embC 4241042 p.Asn394Asp missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.81
embA 4243848 p.Val206Met missense_variant 0.28
embA 4245166 p.Pro645Gln missense_variant 0.27
embA 4245969 p.Pro913Ser missense_variant 0.23
embB 4247646 p.Glu378Ala missense_variant 0.24
ubiA 4269387 p.Glu149Asp missense_variant 0.22
aftB 4269606 c.-770T>C upstream_gene_variant 0.24
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.27
gid 4407588 c.615A>G synonymous_variant 0.24
gid 4407873 c.330G>T synonymous_variant 0.21