TB-Profiler result

Run: ERR2229517
Summary

Run ID: ERR2229517

Sample name:

Date: 31-03-2023 17:16:48

Number of reads: 1190913

Percentage reads mapped: 99.49

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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 0.33
mshA 576482 p.Val379Leu missense_variant 0.13
rpoB 760986 p.Val394Phe missense_variant 0.12
rpoC 766890 p.Glu1174Gly missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777858 p.Glu208Val missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472373 n.528G>T non_coding_transcript_exon_variant 0.12
rrl 1473952 n.296delT non_coding_transcript_exon_variant 0.13
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475005 n.1348C>T non_coding_transcript_exon_variant 0.14
rrl 1475943 n.2286G>T non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155832 p.Asp94His missense_variant 0.11
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289651 c.-410T>C upstream_gene_variant 0.13
kasA 2518688 p.Val192Phe missense_variant 0.12
eis 2714975 p.Ala120Thr missense_variant 0.12
eis 2714985 c.348G>T synonymous_variant 0.12
fbiD 3339641 p.Ala175Asp missense_variant 0.12
rpoA 3877697 p.Thr271Pro missense_variant 0.11
embC 4241713 c.1851G>A synonymous_variant 0.12
embC 4241715 p.Asn618Thr missense_variant 0.12
embC 4241720 p.Thr620Ser missense_variant 0.12
embC 4241724 p.Val621Gly missense_variant 0.12
embC 4241727 p.Phe622Ser missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245842 c.-672G>T upstream_gene_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.4
embB 4246556 p.Ala15Pro missense_variant 0.4
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0