Run ID: ERR4814994
Sample name:
Date: 20-10-2023 07:42:45
Number of reads: 7168035
Percentage reads mapped: 97.3
Strain: lineage2.2.1
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | ||
Isoniazid | R | katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Gly406Asp (1.00) |
Pyrazinamide | ||
Streptomycin | R | rpsL p.Lys43Arg (0.99) |
Fluoroquinolones | ||
Moxifloxacin | ||
Ofloxacin | ||
Levofloxacin | ||
Ciprofloxacin | ||
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | ethA c.1152delT (1.00), ethA c.1152delT (1.00) |
Clofazimine | ||
Para-aminosalicylic_acid | R | folC p.Ser150Gly (1.00) |
Delamanid | ||
Bedaquiline | ||
Linezolid |
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 |
---|---|---|---|---|---|
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.99 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
folC | 2747151 | p.Ser150Gly | missense_variant | 1.0 | para-aminosalicylic_acid |
embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol |
ethA | 4326321 | c.1152delT | frameshift_variant | 1.0 | ethionamide, 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 | 0.96 |
rpoC | 766645 | p.Glu1092Asp | missense_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 | 1471923 | n.78T>C | non_coding_transcript_exon_variant | 0.2 |
rrs | 1471925 | n.80_81insGCAGCTTG | non_coding_transcript_exon_variant | 0.21 |
rrs | 1471928 | n.83T>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1471930 | n.88_89delGA | non_coding_transcript_exon_variant | 0.23 |
rrs | 1471934 | n.89A>G | non_coding_transcript_exon_variant | 0.23 |
rrs | 1471978 | n.133C>T | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472123 | n.278A>T | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472151 | n.306C>A | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472160 | n.315C>T | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472225 | n.380C>G | non_coding_transcript_exon_variant | 0.64 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472498 | n.653C>T | non_coding_transcript_exon_variant | 0.75 |
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.78 |
rrs | 1472558 | n.713G>A | non_coding_transcript_exon_variant | 0.74 |
rrs | 1472569 | n.724G>A | non_coding_transcript_exon_variant | 0.74 |
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472714 | n.869A>G | non_coding_transcript_exon_variant | 0.34 |
rrs | 1472987 | n.1142G>A | non_coding_transcript_exon_variant | 0.45 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1473259 | n.1414C>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473282 | n.1437_1438delCTinsTCA | non_coding_transcript_exon_variant | 0.42 |
rrs | 1473285 | n.1442_1443delCC | non_coding_transcript_exon_variant | 0.39 |
rrs | 1473292 | n.1447G>T | non_coding_transcript_exon_variant | 0.37 |
rrs | 1473293 | n.1448G>T | non_coding_transcript_exon_variant | 0.37 |
rrl | 1474130 | n.473C>T | non_coding_transcript_exon_variant | 0.8 |
rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.83 |
rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.85 |
rrl | 1474182 | n.525C>A | non_coding_transcript_exon_variant | 0.82 |
rrl | 1474183 | n.526T>G | non_coding_transcript_exon_variant | 0.82 |
rrl | 1474184 | n.527C>T | non_coding_transcript_exon_variant | 0.82 |
rrl | 1474185 | n.529delA | non_coding_transcript_exon_variant | 0.82 |
rrl | 1474197 | n.540C>T | non_coding_transcript_exon_variant | 0.86 |
rrl | 1474200 | n.545delT | non_coding_transcript_exon_variant | 0.88 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1474253 | n.596A>T | non_coding_transcript_exon_variant | 0.78 |
rrl | 1474263 | n.606G>A | non_coding_transcript_exon_variant | 0.88 |
rrl | 1474269 | n.612C>T | non_coding_transcript_exon_variant | 0.79 |
rrl | 1474537 | n.880G>A | non_coding_transcript_exon_variant | 0.83 |
rrl | 1474542 | n.885A>C | non_coding_transcript_exon_variant | 0.83 |
rrl | 1474558 | n.901G>A | non_coding_transcript_exon_variant | 0.83 |
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.7 |
rrl | 1474798 | n.1141C>G | non_coding_transcript_exon_variant | 0.7 |
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.58 |
rrl | 1474823 | n.1166C>G | non_coding_transcript_exon_variant | 0.54 |
rrl | 1474824 | n.1167A>G | non_coding_transcript_exon_variant | 0.54 |
rrl | 1474825 | n.1168G>A | non_coding_transcript_exon_variant | 0.54 |
rrl | 1474830 | n.1173A>G | non_coding_transcript_exon_variant | 0.54 |
rrl | 1474837 | n.1180A>G | non_coding_transcript_exon_variant | 0.6 |
rrl | 1475514 | n.1857G>A | non_coding_transcript_exon_variant | 0.76 |
rrl | 1475522 | n.1865A>T | non_coding_transcript_exon_variant | 0.73 |
rrl | 1475525 | n.1868G>A | non_coding_transcript_exon_variant | 0.73 |
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.73 |
rrl | 1475531 | n.1874C>T | non_coding_transcript_exon_variant | 0.73 |
rrl | 1475539 | n.1882A>T | non_coding_transcript_exon_variant | 0.73 |
rrl | 1475542 | n.1885A>G | non_coding_transcript_exon_variant | 0.73 |
rrl | 1475544 | n.1887A>T | non_coding_transcript_exon_variant | 0.73 |
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.73 |
rrl | 1475550 | n.1893A>G | non_coding_transcript_exon_variant | 0.73 |
rrl | 1475713 | n.2056C>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1475753 | n.2096C>G | non_coding_transcript_exon_variant | 0.74 |
rrl | 1475759 | n.2102_2105delCCCGinsT | non_coding_transcript_exon_variant | 0.74 |
rrl | 1475775 | n.2118G>T | non_coding_transcript_exon_variant | 0.72 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.47 |
rrl | 1475883 | n.2226A>T | non_coding_transcript_exon_variant | 0.47 |
rrl | 1475884 | n.2227A>G | non_coding_transcript_exon_variant | 0.47 |
rrl | 1475897 | n.2240T>C | non_coding_transcript_exon_variant | 0.57 |
rrl | 1475900 | n.2243A>G | non_coding_transcript_exon_variant | 0.57 |
rrl | 1475902 | n.2245T>C | non_coding_transcript_exon_variant | 0.58 |
rrl | 1475906 | n.2249C>T | non_coding_transcript_exon_variant | 0.58 |
rrl | 1475975 | n.2318C>T | non_coding_transcript_exon_variant | 0.51 |
rrl | 1475977 | n.2320A>G | non_coding_transcript_exon_variant | 0.51 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.55 |
rrl | 1475997 | n.2340A>T | non_coding_transcript_exon_variant | 0.48 |
rrl | 1476160 | n.2503T>C | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.65 |
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.65 |
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.61 |
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.43 |
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476298 | n.2641C>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476300 | n.2643G>T | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476307 | n.2650A>T | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476309 | n.2652G>T | non_coding_transcript_exon_variant | 0.47 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.7 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476524 | n.2867_2868delCAinsT | non_coding_transcript_exon_variant | 0.56 |
rrl | 1476535 | n.2878G>A | non_coding_transcript_exon_variant | 0.58 |
rrl | 1476539 | n.2882A>G | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.63 |
rrl | 1476573 | n.2916A>T | non_coding_transcript_exon_variant | 0.59 |
rrl | 1476580 | n.2923G>A | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476585 | n.2928A>G | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476594 | n.2937C>T | non_coding_transcript_exon_variant | 0.3 |
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 | 2221988 | p.Leu393Val | missense_variant | 0.33 |
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 | 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 |