Run ID: ERR2124091
Sample name:
Date: 31-03-2023 15:52:05
Number of reads: 7280066
Percentage reads mapped: 99.22
Strain: lineage4.3.4.2
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.3 | Euro-American (LAM) | mainly-LAM | None | 1.0 |
lineage4.3.4 | Euro-American (LAM) | LAM | RD174 | 1.0 |
lineage4.3.4.2 | Euro-American (LAM) | LAM1;LAM4;LAM11 | RD174 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761139 | p.His445Asp | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
embB | 4247429 | p.Met306Val | missense_variant | 0.98 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.98 |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 |
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 | 1472135 | n.290C>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.55 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.46 |
rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472389 | n.544G>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472390 | n.545T>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472697 | n.852T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472707 | n.862A>G | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.65 |
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.68 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472827 | n.982G>T | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472836 | n.991G>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473191 | n.1346C>T | non_coding_transcript_exon_variant | 0.32 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.32 |
rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.32 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.32 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.32 |
rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.15 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ribD | 2987307 | p.Ala157Pro | missense_variant | 0.12 |
Rv2752c | 3065293 | p.Val300Ala | missense_variant | 0.99 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.19 |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 1.0 |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.12 |
embC | 4239763 | c.-100C>T | upstream_gene_variant | 0.98 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4408141 | p.Arg21Pro | missense_variant | 1.0 |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 |