TB-Profiler result

Run: ERR8975402
Summary

Run ID: ERR8975402

Sample name:

Date: 20-10-2023 15:58:02

Number of reads: 2931385

Percentage reads mapped: 99.73

Strain: lineage4.4.1.1;lineage4.3.2.1

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 R gid c.102delG (0.65)
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 0.26
lineage4.4 Euro-American S;T None 0.73
lineage4.3.2 Euro-American (LAM) LAM3 None 0.29
lineage4.4.1 Euro-American (S-type) S;T None 0.74
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.28
lineage4.4.1.1 Euro-American S;Orphans None 0.72
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
gid 4408100 c.102delG frameshift_variant 0.65 streptomycin
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 5520 p.Pro94Leu missense_variant 0.23
gyrA 7222 c.-80C>T upstream_gene_variant 0.3
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 0.71
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619844 c.-47_-46insC upstream_gene_variant 0.72
rpoC 764995 c.1626C>G synonymous_variant 0.32
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102791 c.252A>C synonymous_variant 0.75
ndh 2102990 p.Val18Ala missense_variant 0.77
PPE35 2168479 p.Thr712Pro missense_variant 0.69
PPE35 2169840 p.Gly258Asp missense_variant 0.76
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.79
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.83
Rv3236c 3612665 p.Val151Ala missense_variant 0.77
clpC1 4038287 c.2418C>T synonymous_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328465 c.-992C>T upstream_gene_variant 0.78
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.34