Run ID: ERR1873560
Sample name:
Date: 15-08-2022 11:08:25
Number of reads: 2940426
Percentage reads mapped: 84.44
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.99 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.99 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.98 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.23 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.91 | kanamycin, capreomycin, aminoglycosides, amikacin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288764 | p.Thr160Ala | missense_variant | 1.0 | pyrazinamide |
pncA | 2288943 | p.Thr100Ile | missense_variant | 0.98 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 0.99 | ethambutol |
ethA | 4327347 | p.Gly43Cys | missense_variant | 1.0 | ethionamide |
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 | 491328 | c.546C>G | synonymous_variant | 0.98 |
fgd1 | 491330 | p.Lys183Met | missense_variant | 0.98 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.99 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.98 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764822 | p.Asp485Tyr | missense_variant | 0.99 |
mmpL5 | 775592 | c.2889G>A | synonymous_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 | 0.98 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472112 | n.267C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472122 | n.277G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472129 | n.284G>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472137 | n.292G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472203 | n.358G>A | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472210 | n.365A>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472213 | n.368G>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472215 | n.370A>G | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472234 | n.389T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472236 | n.391C>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472573 | n.728C>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.28 |
rrs | 1472596 | n.751G>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472614 | n.769G>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.3 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.32 |
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 | 0.48 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.12 |
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 | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.26 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
Rv3083 | 3449315 | p.Trp271* | stop_gained | 0.98 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.98 |
rpoA | 3878641 | c.-135delG | upstream_gene_variant | 0.1 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.22 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4247717 | p.Leu402Val | missense_variant | 1.0 |
embB | 4249397 | p.Ala962Pro | missense_variant | 0.17 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 |
whiB6 | 4338365 | p.Cys53Arg | missense_variant | 0.98 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.97 |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.98 |