Run ID: SRR10315595
Sample name:
Date: 02-04-2023 17:11:47
Number of reads: 9031886
Percentage reads mapped: 92.88
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 |
---|---|---|---|---|---|
gyrB | 6738 | p.Thr500Asn | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
gyrA | 7572 | p.Ser91Pro | missense_variant | 1.0 | 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 |
fabG1 | 1673423 | c.-17G>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
tlyA | 1918521 | c.585_588delTGGG | frameshift_variant | 1.0 | capreomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2289202 | p.Cys14Arg | missense_variant | 1.0 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
embB | 4248002 | p.Gln497Lys | 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 |
mshA | 576108 | p.Ala254Gly | missense_variant | 0.17 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764817 | p.Val483Gly | missense_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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474147 | n.490A>G | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475602 | n.1945G>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476252 | n.2595T>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476266 | n.2609G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476279 | n.2622G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476281 | n.2624T>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476301 | n.2644A>C | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476356 | n.2699C>G | non_coding_transcript_exon_variant | 0.2 |
rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476404 | n.2747G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476474 | n.2817C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.23 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476515 | n.2858C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.16 |
rrl | 1476540 | n.2883C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476544 | n.2887T>A | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476577 | n.2920T>C | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476585 | n.2928A>G | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476586 | n.2929C>T | non_coding_transcript_exon_variant | 0.11 |
rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476603 | n.2946G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476612 | n.2955G>C | non_coding_transcript_exon_variant | 0.13 |
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 | 0.96 |
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 |
rpoA | 3878630 | c.-123G>C | upstream_gene_variant | 0.11 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
aftB | 4267229 | p.Trp536Cys | missense_variant | 0.12 |
aftB | 4267647 | p.Asp397Gly | 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 |