Run ID: ERR027451
Sample name:
Date: 20-10-2023 23:28:14
Number of reads: 3624715
Percentage reads mapped: 97.78
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (1.00), rpoC p.Asp485Asn (1.00) |
Isoniazid | R | inhA c.-154G>A (0.62), katG p.Ile335Val (1.00), katG p.Ser315Thr (1.00) |
Ethambutol | R | embB p.Gln497Arg (1.00) |
Pyrazinamide | R | pncA p.Thr135Pro (0.97) |
Streptomycin | R | rpsL p.Lys43Arg (1.00) |
Fluoroquinolones | R | gyrA p.Asp94Gly (0.95) |
Moxifloxacin | R | gyrA p.Asp94Gly (0.95) |
Ofloxacin | R | gyrA p.Asp94Gly (0.95) |
Levofloxacin | R | gyrA p.Asp94Gly (0.95) |
Ciprofloxacin | R | gyrA p.Asp94Gly (0.95) |
Aminoglycosides | R | rrs n.1401A>G (0.97) |
Amikacin | R | rrs n.1401A>G (0.97) |
Capreomycin | R | rrs n.1401A>G (0.97) |
Kanamycin | R | rrs n.1401A>G (0.97) |
Cycloserine | ||
Ethionamide | R | inhA c.-154G>A (0.62) |
Clofazimine | ||
Para-aminosalicylic_acid | ||
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 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.95 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpoC | 764822 | p.Asp485Asn | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.97 | kanamycin, capreomycin, aminoglycosides, amikacin |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.62 | isoniazid, ethionamide |
katG | 2155109 | p.Ile335Val | missense_variant | 1.0 | isoniazid |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288839 | p.Thr135Pro | missense_variant | 0.97 | pyrazinamide |
embB | 4248003 | p.Gln497Arg | missense_variant | 1.0 | ethambutol |
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 | 0.97 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.94 |
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1302917 | c.-14_-13insA | 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 | 1472129 | n.284G>C | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472137 | n.292G>A | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.6 |
rrs | 1472203 | n.358G>A | non_coding_transcript_exon_variant | 0.49 |
rrs | 1472210 | n.365A>C | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472213 | n.368G>C | non_coding_transcript_exon_variant | 0.35 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472378 | n.533G>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472379 | n.534T>G | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472382 | n.537G>A | non_coding_transcript_exon_variant | 0.31 |
rrs | 1472400 | n.555C>T | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472591 | n.746G>A | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.4 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.42 |
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472895 | n.1050C>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1473035 | n.1190G>A | non_coding_transcript_exon_variant | 0.39 |
rrs | 1473053 | n.1208T>A | non_coding_transcript_exon_variant | 0.46 |
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.46 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.4 |
rrs | 1473080 | n.1235C>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.3 |
rrs | 1473201 | n.1356_1357delACinsT | non_coding_transcript_exon_variant | 0.34 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.34 |
rrs | 1473328 | n.1483C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473352 | n.1507C>T | non_coding_transcript_exon_variant | 0.3 |
rrl | 1474844 | n.1187G>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474864 | n.1207C>T | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474866 | n.1209C>A | non_coding_transcript_exon_variant | 0.2 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.21 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.22 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.39 |
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476268 | n.2611A>T | non_coding_transcript_exon_variant | 0.35 |
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.38 |
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.49 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.44 |
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.46 |
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.37 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.51 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.41 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.29 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834776 | p.Ala412Val | missense_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 | 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 |
fbiB | 3640879 | c.-656C>T | upstream_gene_variant | 1.0 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embA | 4243598 | c.366G>A | synonymous_variant | 1.0 |
embB | 4247872 | c.1359C>T | synonymous_variant | 1.0 |
ethA | 4326474 | p.Pro334Ala | missense_variant | 1.0 |
whiB6 | 4338326 | p.Ala66Thr | 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 |