TB-Profiler result

Run: ERR2510764
Summary

Run ID: ERR2510764

Sample name:

Date: 31-03-2023 18:55:43

Number of reads: 1388372

Percentage reads mapped: 90.97

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrB 6735 p.Asn499Thr missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781821 p.Lys88Gln missense_variant 1.0 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.15 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289038 p.Trp68* stop_gained 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4247729 p.Gly406Cys missense_variant 1.0 ethambutol
ethA 4326969 c.504delC frameshift_variant 1.0 ethionamide
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 5078 c.-162_-161insG upstream_gene_variant 0.36
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.22
rpoB 759955 p.Val50Gly missense_variant 1.0
rpoC 765713 p.Thr782Ala missense_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
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.13
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.13
rrl 1473845 n.188G>A non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474074 n.417C>T non_coding_transcript_exon_variant 0.11
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.11
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.11
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.11
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 0.11
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.12
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.11
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.12
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.12
rrl 1474630 n.973T>C non_coding_transcript_exon_variant 0.12
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.12
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.12
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.12
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.12
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.12
rrl 1474660 n.1003G>A non_coding_transcript_exon_variant 0.11
rrl 1475244 n.1587A>T non_coding_transcript_exon_variant 0.1
rrl 1475812 n.2157delA non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.15
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.15
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.17
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.17
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.17
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.17
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.17
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.18
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087251 c.434dupG frameshift_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fbiA 3640901 p.Gln120Arg missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0