Run ID: SRR1165243
Sample name:
Date: 02-04-2023 23:50:09
Number of reads: 3789096
Percentage reads mapped: 78.45
Strain: lineage2.2.2
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 |
lineage2.2.2 | East-Asian (Beijing) | Beijing-RD105/RD207 | RD105;RD207 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7581 | p.Asp94His | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761110 | p.Asp435Val | missense_variant | 1.0 | rifampicin |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 0.99 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.98 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673423 | c.-17G>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288724 | c.517dupG | frameshift_variant | 1.0 | pyrazinamide, pyrazinamide |
alr | 3841083 | p.Leu113Arg | missense_variant | 1.0 | cycloserine |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
ethA | 4326333 | p.Ala381Pro | missense_variant | 1.0 | ethionamide |
gid | 4407967 | p.Leu79Ser | missense_variant | 1.0 | streptomycin |
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 |
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 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
Rv1258c | 1407135 | c.203_205dupACT | conservative_inframe_insertion | 0.13 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472113 | n.268T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472129 | n.284G>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472137 | n.292G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472151 | n.306C>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472203 | n.358G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472210 | n.365A>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472213 | n.368G>C | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472215 | n.370A>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472544 | n.699C>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472779 | n.934G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472786 | n.941C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474790 | n.1133C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1474798 | n.1141C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474804 | n.1147C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474827 | n.1170C>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1474831 | n.1174A>C | non_coding_transcript_exon_variant | 0.27 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474896 | n.1239A>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474902 | n.1245T>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474904 | n.1247G>C | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474913 | n.1256T>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.21 |
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 |
Rv1979c | 2221939 | p.Arg409Gln | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>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 | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.97 |
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 |