TB-Profiler result

Run: ERR037547

Summary

Run ID: ERR037547

Sample name:

Date: 19-10-2023 17:38:21

Number of reads: 19657066

Percentage reads mapped: 99.39

Strain: lineage4.3.4.1;lineage1.1.3.2

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 0.9
lineage4.3 Euro-American (LAM) mainly-LAM None 0.93
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.07
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.12
lineage4.3.4 Euro-American (LAM) LAM RD174 0.91
lineage1.1.3.2 Indo-Oceanic NA RD239 0.09
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.9
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 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619695 c.-196G>A upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.13
PPE35 2167983 p.Gly877Asp missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 0.91
fbiB 3640614 c.-921C>T upstream_gene_variant 0.93
clpC1 4038287 c.2418C>T synonymous_variant 0.88
clpC1 4040517 p.Val63Ala missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245329 c.2097A>G synonymous_variant 0.91
aftB 4269411 c.-575T>C upstream_gene_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407780 c.423G>A synonymous_variant 0.13
gid 4407873 c.330G>T synonymous_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 0.9