TB-Profiler result

Run: ERR7363097
Summary

Run ID: ERR7363097

Sample name:

Date: 19-05-2023 14:25:36

Number of reads: 2339719

Percentage reads mapped: 99.66

Strain: lineage4.4.1.1;lineage4.3.4.2

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 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.1
lineage4.4 Euro-American S;T None 0.89
lineage4.4.1 Euro-American (S-type) S;T None 0.89
lineage4.3.4 Euro-American (LAM) LAM RD174 0.11
lineage4.4.1.1 Euro-American S;Orphans None 0.89
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.12
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 6140 p.Val301Leu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 0.98
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.75
PPE35 2169840 p.Gly258Asp missense_variant 0.85
PPE35 2170048 p.Leu189Val missense_variant 0.1
PPE35 2170065 p.Ala183Gly missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747605 c.-7C>G upstream_gene_variant 0.82
pepQ 2860518 c.-100C>T upstream_gene_variant 0.16
thyA 3073868 p.Thr202Ala missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.38
Rv3083 3448608 c.105G>A synonymous_variant 0.95
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475113 c.1107G>C synonymous_variant 0.14
Rv3236c 3612009 p.Ala370Thr missense_variant 0.19
Rv3236c 3612665 p.Val151Ala missense_variant 0.9
Rv3236c 3612737 p.Ile127Thr missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243577 c.345C>T synonymous_variant 0.95
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246584 p.Arg24Pro missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.21