TB-Profiler result

Run: ERR4800116
Summary

Run ID: ERR4800116

Sample name:

Date: 01-04-2023 09:35:48

Number of reads: 2807005

Percentage reads mapped: 99.74

Strain: lineage4.3.3

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 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.98
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 7570 p.Ala90Val missense_variant 0.26 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760314 p.Val170Phe missense_variant 0.97 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.96 isoniazid
pncA 2288821 c.419_420dupGC frameshift_variant 0.66 pyrazinamide
pncA 2289075 c.166dupG frameshift_variant 0.12 pyrazinamide
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 0.98
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575909 p.Leu188Val missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.97
rpoC 765847 p.Asn826Lys missense_variant 0.98
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.96
thyA 3073868 p.Thr202Ala missense_variant 0.97
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 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247495 p.Asp328His missense_variant 0.99
whiB6 4338367 p.Leu52Gln missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407777 p.Leu142Phe missense_variant 0.97
gid 4408156 p.Leu16Arg missense_variant 0.98