TB-Profiler result

Run: ERR1034757
Summary

Run ID: ERR1034757

Sample name:

Date: 20-10-2023 23:15:20

Number of reads: 15516671

Percentage reads mapped: 99.6

Strain: lineage4.3.4.1;lineage4.3.3

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.Ala286Val (0.51), rpoB p.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.40)
Pyrazinamide R pncA p.Asp49Asn (0.50)
Streptomycin R rpsL p.Lys88Thr (0.58), gid c.180delA (0.47)
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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.55
lineage4.3.4 Euro-American (LAM) LAM RD174 0.45
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.45
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 760663 p.Ala286Val missense_variant 0.51 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Thr missense_variant 0.58 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289097 p.Asp49Asn missense_variant 0.5 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.4 ethambutol
gid 4408022 c.180delA frameshift_variant 0.47 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.55
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761880 p.Ala692Thr missense_variant 0.53
rpoC 764805 p.Gln479Arg missense_variant 0.45
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765590 p.Arg741Ser missense_variant 0.48
rpoC 765804 p.Thr812Ile missense_variant 0.52
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
rpsA 1834378 c.837T>C synonymous_variant 0.41
rpsA 1834836 p.Met432Thr missense_variant 0.51
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154459 c.1653C>T synonymous_variant 0.55
Rv1979c 2223123 c.42G>A synonymous_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.53
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.47
clpC1 4038287 c.2418C>T synonymous_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407720 c.483C>G synonymous_variant 0.6
gid 4408003 p.Asp67Gly missense_variant 0.53
gid 4408156 p.Leu16Arg missense_variant 1.0