TB-Profiler result

Run: ERR1035070
Summary

Run ID: ERR1035070

Sample name:

Date: 20-10-2023 23:36:20

Number of reads: 8473348

Percentage reads mapped: 99.5

Strain: lineage4.4.1.1;lineage4.3.2.1

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Trp (0.48), rpoB p.Ser450Leu (0.52)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embA c.-12C>T (0.53), embB p.Gln497Arg (0.46)
Pyrazinamide R pncA p.Val130Ala (0.47), pncA p.Leu85Pro (0.51)
Streptomycin R gid c.102delG (0.49)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
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 0.53
lineage4.4 Euro-American S;T None 0.49
lineage4.3.2 Euro-American (LAM) LAM3 None 0.52
lineage4.4.1 Euro-American (S-type) S;T None 0.49
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.53
lineage4.4.1.1 Euro-American S;Orphans None 0.5
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 0.48 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.52 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288853 p.Val130Ala missense_variant 0.47 pyrazinamide
pncA 2288988 p.Leu85Pro missense_variant 0.51 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.53 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.46 ethambutol
gid 4408100 c.102delG frameshift_variant 0.49 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 0.54
gyrA 7222 c.-80C>T upstream_gene_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 0.45
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576672 c.1327_1328dupCG frameshift_variant 0.34
rpoB 762793 c.2993_2998dupCCGACG disruptive_inframe_insertion 0.36
rpoC 764995 c.1626C>G synonymous_variant 0.55
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 0.56
mmpL5 778510 c.-30T>C upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304345 p.Asp472Ala missense_variant 0.51
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.49
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.46
PPE35 2168479 p.Thr712Pro missense_variant 0.51
PPE35 2169840 p.Gly258Asp missense_variant 0.55
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064552 c.1639delC frameshift_variant 0.52
thyA 3073868 p.Thr202Ala missense_variant 0.48
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086944 c.126dupC frameshift_variant 0.43
Rv3083 3448608 c.105G>A synonymous_variant 0.5
Rv3083 3449108 p.Gly202Asp missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.43
Rv3236c 3612665 p.Val151Ala missense_variant 0.42
clpC1 4038287 c.2418C>T synonymous_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4327059 p.Gly139Cys missense_variant 0.47
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407760 p.Trp148Ser missense_variant 0.48
gid 4408156 p.Leu16Arg missense_variant 0.44