Run ID: ERR1873563
Sample name:
Date: 15-08-2022 11:08:15
Number of reads: 2425648
Percentage reads mapped: 82.04
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 | 0.99 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.31 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin, capreomycin, aminoglycosides, amikacin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
inhA | 1674782 | p.Ile194Thr | missense_variant | 1.0 | isoniazid, ethionamide |
pncA | 2288839 | p.Thr135Pro | missense_variant | 1.0 | pyrazinamide |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol |
ethR | 4327831 | p.Ala95Thr | 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 | 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 |
rpoC | 763555 | c.186C>T | 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 | 778979 | c.-74G>T | upstream_gene_variant | 0.96 |
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 | 0.97 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472203 | n.358G>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472210 | n.365A>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472213 | n.368G>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472215 | n.370A>G | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472234 | n.389T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472236 | n.391C>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472240 | n.395G>A | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472570 | n.725G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472573 | n.728C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472596 | n.751G>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472614 | n.769G>T | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472767 | n.922G>A | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.14 |
rrs | 1473226 | n.1381C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.25 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.22 |
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476524 | n.2867C>A | 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 | 0.14 |
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.11 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.98 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.98 |
PPE35 | 2169320 | p.Leu431Phe | missense_variant | 0.28 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
ribD | 2987307 | p.Ala157Pro | missense_variant | 0.47 |
thyA | 3073806 | c.666C>G | synonymous_variant | 0.38 |
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 | 0.97 |
rpoA | 3878641 | c.-135delG | upstream_gene_variant | 0.1 |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.28 |
embC | 4239842 | c.-21C>A | upstream_gene_variant | 0.17 |
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 | 0.95 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 0.98 |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 |