TB-Profiler result

Run: ERR4820845
Summary

Run ID: ERR4820845

Sample name:

Date: 01-04-2023 16:54:43

Number of reads: 1262480

Percentage reads mapped: 89.21

Strain: lineage4.8

Drug-resistance: MDR-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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288808 c.433delG frameshift_variant 1.0 pyrazinamide
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 9432 p.Leu711Met missense_variant 1.0
ccsA 620358 c.468C>T synonymous_variant 1.0
rpoB 761593 p.Ala596Gly missense_variant 1.0
rpoC 763058 c.-312C>T upstream_gene_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776995 p.Ser496Pro missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406631 p.Ala237Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.5
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.5
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.5
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.6
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.6
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.8
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 1.0
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 1.0
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 1.0
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.8
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 1.0
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 1.0
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.75
rrs 1472553 n.708C>T non_coding_transcript_exon_variant 0.86
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.88
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.88
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.88
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.88
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 1.0
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 1.0
rrs 1472584 n.739A>G non_coding_transcript_exon_variant 1.0
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 1.0
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 1.0
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0
rrl 1473733 n.76C>T non_coding_transcript_exon_variant 1.0
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168105 c.2508C>T synonymous_variant 0.11
PPE35 2168466 p.Leu716His missense_variant 0.1
Rv1979c 2223006 c.158delT frameshift_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289917 c.-676G>T upstream_gene_variant 0.1
Rv2752c 3066055 p.Gly46Val missense_variant 0.11
ald 3086966 p.Asp49Glu missense_variant 1.0
clpC1 4038749 c.1955delG frameshift_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethR 4327636 c.89delT frameshift_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0