TB-Profiler result

Run: ERR2515482
Summary

Run ID: ERR2515482

Sample name:

Date: 31-03-2023 20:57:38

Number of reads: 574674

Percentage reads mapped: 99.76

Strain: lineage4.8

Drug-resistance: RR-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
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
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
rpoB 762201 p.Lys799Gln missense_variant 1.0
rpoC 765927 p.Thr853Ser missense_variant 1.0
rpoC 766544 p.Glu1059Lys missense_variant 0.11
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 1473733 n.76C>T non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474564 n.907G>A non_coding_transcript_exon_variant 0.11
rrl 1475037 n.1380T>A non_coding_transcript_exon_variant 0.17
rrl 1475481 n.1824C>T non_coding_transcript_exon_variant 0.12
rrl 1476274 n.2617G>A non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102813 p.Arg77Pro missense_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.12
PPE35 2170415 c.198A>G synonymous_variant 0.17
PPE35 2170532 c.81G>A synonymous_variant 0.12
PPE35 2170655 c.-43G>T upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518766 p.Thr218Ala missense_variant 0.11
ribD 2986778 c.-61G>A upstream_gene_variant 1.0
Rv3236c 3613295 c.-179G>T upstream_gene_variant 0.11
fbiB 3641823 p.Asn97Asp missense_variant 0.13
rpoA 3878402 p.Asn36Tyr missense_variant 0.15
embC 4240147 c.285C>T synonymous_variant 1.0
embC 4241643 p.Ala594Glu missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244669 c.1437G>T synonymous_variant 0.1
embA 4245422 c.2190G>A synonymous_variant 0.1
aftB 4267149 p.Glu563Gly missense_variant 1.0
aftB 4267155 p.Gln561Arg missense_variant 1.0
aftB 4268503 p.Gly112Ser missense_variant 0.2
aftB 4268544 p.Leu98Pro missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408239 c.-37A>G upstream_gene_variant 0.12
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0