TB-Profiler result

Run: ERR4798238
Summary

Run ID: ERR4798238

Sample name:

Date: 20-10-2023 02:50:14

Number of reads: 3262125

Percentage reads mapped: 99.68

Strain: lineage4.3.3;lineage3

Drug-resistance: MDR-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.Ser450Leu (0.73)
Isoniazid R katG p.Ser315Thr (0.56)
Ethambutol R embB p.Met306Val (0.68)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.60)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.67)
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.71
lineage4 Euro-American LAM;T;S;X;H None 0.28
lineage4.3 Euro-American (LAM) mainly-LAM None 0.31
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.33
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
rpoB 761155 p.Ser450Leu missense_variant 0.73 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.6 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.56 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.67 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.68 ethambutol
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.67
rpoB 759746 c.-61C>T upstream_gene_variant 0.74
rpoC 762434 c.-936T>G upstream_gene_variant 0.7
rpoC 763031 c.-339T>C upstream_gene_variant 0.6
rpoC 764817 p.Val483Ala missense_variant 0.66
rpoC 764995 c.1626C>G synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.8
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.68
katG 2156196 c.-85C>T upstream_gene_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 0.68
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.66
kasA 2518919 p.Gly269Ser missense_variant 0.4
ahpC 2726105 c.-88G>A upstream_gene_variant 0.65
folC 2746340 p.Ala420Val missense_variant 0.36
thyA 3073868 p.Thr202Ala missense_variant 0.33
thyA 3074407 p.Thr22Asn missense_variant 0.62
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 0.7
clpC1 4038287 c.2418C>T synonymous_variant 0.24
embC 4242075 p.Arg738Gln missense_variant 0.7
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4327229 p.Leu82Arg missense_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.59
gid 4408156 p.Leu16Arg missense_variant 0.29