Run ID: ERR5865302
Sample name:
Date: 01-04-2023 23:55:53
Number of reads: 1866693
Percentage reads mapped: 75.74
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoC | 764822 | p.Asp485Asn | missense_variant | 0.97 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.4 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289052 | p.Tyr64Asp | missense_variant | 1.0 | pyrazinamide |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 1.0 | kanamycin |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 1.0 | 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 | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472579 | n.734G>C | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472580 | n.735C>T | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.24 |
rrs | 1473130 | n.1285G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473147 | n.1302G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473150 | n.1305T>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473161 | n.1316A>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473164 | n.1319C>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473199 | n.1356delA | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475783 | n.2126T>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.53 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.15 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pepQ | 2860462 | c.-44C>G | upstream_gene_variant | 1.0 |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 1.0 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 0.96 |
embA | 4243346 | c.114A>G | synonymous_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |