TB-Profiler result

Run: ERR4813120
Summary

Run ID: ERR4813120

Sample name:

Date: 01-04-2023 12:33:07

Number of reads: 3040675

Percentage reads mapped: 99.64

Strain: lineage4.3.2;lineage4.1.1

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
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
lineage4.1 Euro-American T;X;H None 0.77
lineage4.3.2 Euro-American (LAM) LAM3 None 0.27
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.73
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 7581 p.Asp94Asn missense_variant 0.72 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761101 p.Gln432Pro missense_variant 0.29 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.75 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288764 p.Thr160Pro missense_variant 0.27 pyrazinamide
pncA 2289213 p.Gln10Pro missense_variant 0.7 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 0.76 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
gyrB 6052 p.Ile271Met missense_variant 0.7
gyrB 7221 p.Ser661Thr missense_variant 0.74
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.25
rpoC 765150 p.Gly594Glu missense_variant 0.74
rpoC 765926 p.Thr853Ala missense_variant 0.34
rpoC 767058 p.Thr1230Ile missense_variant 0.72
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 0.69
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.23
inhA 1673865 c.-337C>T upstream_gene_variant 0.64
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.76
embB 4249408 c.2895G>A synonymous_variant 0.7
ethA 4326900 p.Pro192Ser missense_variant 0.75
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407721 p.Ala161Gly missense_variant 0.24
gid 4407980 p.Pro75Ser missense_variant 0.67
gid 4408050 p.Asn51Lys missense_variant 0.33
gid 4408156 p.Leu16Arg missense_variant 0.39