TB-Profiler result

Run: ERR4829767
Summary

Run ID: ERR4829767

Sample name:

Date: 01-04-2023 19:40:36

Number of reads: 2488572

Percentage reads mapped: 99.09

Strain: lineage4.8

Drug-resistance: HR-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
katG 2156121 c.-10A>C upstream_gene_variant 0.99 isoniazid
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
mshA 576108 p.Ala254Gly missense_variant 0.19
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 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474069 n.412G>A non_coding_transcript_exon_variant 0.15
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.17
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.18
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.17
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.25
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.14
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.14
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.14
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.11
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.1
rrl 1476547 n.2890C>A non_coding_transcript_exon_variant 0.11
rrl 1476704 n.3053dupC non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.4
aftB 4267149 p.Glu563Gly missense_variant 1.0
aftB 4267155 p.Gln561Arg missense_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