Run ID: ERR2517627
Sample name:
Date: 31-03-2023 22:20:42
Number of reads: 3074602
Percentage reads mapped: 94.85
Strain: lineage4.8
Drug-resistance: RR-TB
Drug | Resistance | Supporting mutations |
---|
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 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761089 | p.Ser428Thr | missense_variant | 0.11 | rifampicin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
rpoB | 760127 | p.Asp107Glu | missense_variant | 1.0 |
rpoB | 761084 | c.1278C>A | synonymous_variant | 0.11 |
rpoB | 762053 | c.2247T>C | synonymous_variant | 0.11 |
rpoB | 762057 | p.Ile751Val | missense_variant | 0.11 |
rpoB | 762062 | c.2256T>C | synonymous_variant | 0.11 |
rpoB | 762071 | p.Asp755Glu | missense_variant | 0.11 |
rpoB | 762080 | c.2274G>C | synonymous_variant | 0.1 |
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 | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472122 | n.277G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472123 | n.278A>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472124 | n.279C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472155 | n.310C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473276 | n.1431A>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473288 | n.1443C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476429 | n.2772A>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2290199 | c.-959delA | upstream_gene_variant | 1.0 |
Rv2752c | 3065019 | c.1173C>T | synonymous_variant | 1.0 |
Rv3083 | 3448497 | c.-7T>A | upstream_gene_variant | 1.0 |
Rv3083 | 3448500 | c.-4A>G | upstream_gene_variant | 1.0 |
Rv3083 | 3448501 | c.-3G>T | upstream_gene_variant | 1.0 |
rpoA | 3878561 | c.-54C>A | upstream_gene_variant | 0.22 |
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 |