TB-Profiler result

Run: ERR2516687
Summary

Run ID: ERR2516687

Sample name:

Date: 31-03-2023 21:40:52

Number of reads: 3462190

Percentage reads mapped: 99.81

Strain: lineage4.3.4.2

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 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
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.Asp94Ala missense_variant 0.62 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289061 p.Thr61Pro missense_variant 0.11 pyrazinamide
pncA 2289252 c.-11A>C upstream_gene_variant 0.69 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 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 7615 p.Leu105Arg missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
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
rrl 1474943 n.1286A>G non_coding_transcript_exon_variant 0.1
rrl 1475019 n.1362T>C non_coding_transcript_exon_variant 0.12
rrl 1475940 n.2283C>T non_coding_transcript_exon_variant 0.13
rpsA 1834234 c.693G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2154974 p.Thr380Pro missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289162 p.Leu27Arg missense_variant 0.22
folC 2747481 p.Glu40Lys missense_variant 1.0
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.23
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 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.29
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247884 c.1371C>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408061 p.His48Tyr missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0