TB-Profiler result

Run: ERR181977
Summary

Run ID: ERR181977

Sample name:

Date: 20-10-2023 22:39:29

Number of reads: 4162818

Percentage reads mapped: 99.41

Strain: lineage4.3.4.2.1;lineage4.1.2;lineage1.1.2

Drug-resistance: Other

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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 R ethR p.Phe110Leu (0.16)
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 0.2
lineage1 Indo-Oceanic EAI RD239 0.79
lineage4.3 Euro-American (LAM) mainly-LAM None 0.06
lineage4.1 Euro-American T;X;H None 0.1
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.8
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.8
lineage4.1.2 Euro-American T;H None 0.12
lineage4.3.4 Euro-American (LAM) LAM RD174 0.06
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.07
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.08
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
ethR 4327876 p.Phe110Leu missense_variant 0.16 ethionamide
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 0.74
gyrB 6124 c.885C>T synonymous_variant 0.79
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.76
gyrA 9143 c.1842T>C synonymous_variant 0.73
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.8
rpoB 760115 c.309C>T synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.68
rpoC 763884 p.Ala172Val missense_variant 0.8
rpoC 763886 c.517C>A synonymous_variant 0.79
rpoC 765171 p.Pro601Leu missense_variant 0.77
rpoC 765988 c.2619G>A synonymous_variant 0.84
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.84
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 0.84
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 0.79
PPE35 2167926 p.Leu896Ser missense_variant 0.74
PPE35 2167983 p.Gly877Asp missense_variant 0.73
Rv1979c 2222308 p.Asp286Gly missense_variant 0.79
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 0.75
ahpC 2726051 c.-142G>A upstream_gene_variant 0.75
ahpC 2726468 c.276G>A synonymous_variant 0.76
Rv2752c 3064632 c.1560C>T synonymous_variant 0.81
thyX 3067491 p.Ala152Val missense_variant 0.82
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.71
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.84
fprA 3475023 c.1017G>A synonymous_variant 0.85
fprA 3475159 p.Asn385Asp missense_variant 0.79
fbiA 3640446 c.-97A>T upstream_gene_variant 0.74
alr 3840263 c.1158C>T synonymous_variant 0.17
alr 3840719 c.702A>G synonymous_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.81
embC 4240671 p.Thr270Ile missense_variant 0.81
embC 4241042 p.Asn394Asp missense_variant 0.75
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.1
embA 4243848 p.Val206Met missense_variant 0.81
embA 4245969 p.Pro913Ser missense_variant 0.77
embB 4247646 p.Glu378Ala missense_variant 0.72
aftB 4267091 c.1746C>A synonymous_variant 0.17
ubiA 4269387 p.Glu149Asp missense_variant 0.7
aftB 4269606 c.-770T>C upstream_gene_variant 0.8
ethA 4326851 p.Ser208Leu missense_variant 0.75
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.73
gid 4407588 c.615A>G synonymous_variant 0.77
gid 4407873 c.330G>T synonymous_variant 0.8
gid 4408156 p.Leu16Arg missense_variant 0.12