Run ID: ERR11138607
Sample name:
Date: 16-04-2023 18:20:25
Number of reads: 4592906
Percentage reads mapped: 96.5
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|---|---|
Rifampicin | R | rpoB p.Ser450Leu (0.94) |
Isoniazid | R | fabG1 c.-15C>T (1.00) |
Ethambutol | R | embB p.Met306Val (0.95) |
Pyrazinamide | ||
Streptomycin | R | rrs n.517C>T (0.92) |
Fluoroquinolones | R | gyrA p.Asp94Gly (0.99) |
Moxifloxacin | R | gyrA p.Asp94Gly (0.99) |
Ofloxacin | R | gyrA p.Asp94Gly (0.99) |
Levofloxacin | R | gyrA p.Asp94Gly (0.99) |
Ciprofloxacin | R | gyrA p.Asp94Gly (0.99) |
Aminoglycosides | ||
Amikacin | ||
Capreomycin | ||
Kanamycin | ||
Cycloserine | ||
Ethionamide | R | fabG1 c.-15C>T (1.00) |
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 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.99 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.94 | rifampicin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.92 | streptomycin |
fabG1 | 1673425 | c.-15C>T | upstream_gene_variant | 1.0 | isoniazid, ethionamide |
embB | 4247429 | p.Met306Val | missense_variant | 0.95 | 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 | 9182 | c.1881T>C | synonymous_variant | 0.14 |
gyrA | 9191 | c.1890G>C | synonymous_variant | 0.15 |
gyrA | 9200 | c.1899A>G | synonymous_variant | 0.18 |
gyrA | 9204 | p.Ser635Thr | missense_variant | 0.2 |
gyrA | 9224 | c.1923C>T | synonymous_variant | 0.18 |
gyrA | 9230 | c.1929T>C | synonymous_variant | 0.16 |
gyrA | 9233 | c.1932C>G | synonymous_variant | 0.16 |
gyrA | 9239 | c.1938C>T | synonymous_variant | 0.16 |
gyrA | 9252 | p.Val651Ile | missense_variant | 0.15 |
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 |
rpoB | 760328 | c.522G>C | synonymous_variant | 0.13 |
rpoB | 760340 | c.534G>T | synonymous_variant | 0.12 |
rpoB | 760925 | c.1119T>C | synonymous_variant | 0.12 |
rpoB | 760928 | c.1122G>C | synonymous_variant | 0.12 |
rpoB | 760931 | c.1125C>G | synonymous_variant | 0.12 |
rpoB | 760934 | c.1128C>T | synonymous_variant | 0.12 |
rpoB | 760946 | c.1140A>G | synonymous_variant | 0.15 |
rpoB | 762008 | c.2202C>T | synonymous_variant | 0.15 |
rpoB | 762014 | c.2208C>T | synonymous_variant | 0.14 |
rpoB | 762017 | c.2211A>G | synonymous_variant | 0.13 |
rpoB | 762053 | c.2247T>C | synonymous_variant | 0.12 |
rpoB | 762246 | c.2440C>T | synonymous_variant | 0.14 |
rpoB | 762254 | c.2448T>G | synonymous_variant | 0.12 |
rpoB | 762257 | c.2451C>G | synonymous_variant | 0.12 |
rpoB | 762266 | c.2460T>C | synonymous_variant | 0.12 |
rpoB | 762284 | c.2478G>C | synonymous_variant | 0.13 |
rpoB | 762293 | c.2487T>C | synonymous_variant | 0.13 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.99 |
rpoC | 763774 | c.405G>C | synonymous_variant | 0.12 |
rpoC | 764248 | c.879C>G | synonymous_variant | 0.12 |
rpoC | 764257 | c.888G>C | synonymous_variant | 0.14 |
rpoC | 764266 | c.897T>C | synonymous_variant | 0.13 |
rpoC | 764269 | c.900G>C | synonymous_variant | 0.14 |
rpoC | 764272 | c.903G>C | synonymous_variant | 0.14 |
rpoC | 764278 | c.909A>G | synonymous_variant | 0.16 |
rpoC | 765700 | c.2331T>C | synonymous_variant | 0.13 |
rpoC | 765850 | c.2481G>C | synonymous_variant | 0.12 |
rpoC | 765883 | c.2514C>G | synonymous_variant | 0.12 |
rpoC | 766726 | c.3357T>C | synonymous_variant | 0.15 |
rpoC | 766738 | c.3369G>C | synonymous_variant | 0.15 |
rpoC | 766765 | c.3396A>C | synonymous_variant | 0.15 |
rpoC | 766774 | c.3405T>C | synonymous_variant | 0.14 |
rpoC | 766861 | c.3492G>C | synonymous_variant | 0.13 |
rpoC | 766864 | c.3495G>C | synonymous_variant | 0.13 |
rpoC | 766900 | c.3531T>C | synonymous_variant | 0.17 |
rpoC | 766933 | c.3564A>G | synonymous_variant | 0.16 |
rpoC | 766945 | c.3576A>G | synonymous_variant | 0.13 |
rpoC | 767033 | c.3664_3666delTCGinsAGC | synonymous_variant | 0.13 |
rpoC | 767059 | c.3690T>G | synonymous_variant | 0.13 |
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 |
rpsL | 781682 | c.123T>C | synonymous_variant | 0.12 |
rpsL | 781700 | c.141G>C | synonymous_variant | 0.13 |
rpsL | 781703 | c.144G>T | synonymous_variant | 0.12 |
rpsL | 781715 | c.156T>C | synonymous_variant | 0.15 |
rpsL | 781728 | c.169T>C | synonymous_variant | 0.15 |
rpsL | 781736 | c.177T>C | synonymous_variant | 0.15 |
rpsL | 781742 | c.183C>T | synonymous_variant | 0.15 |
rpsL | 781748 | c.189C>G | synonymous_variant | 0.14 |
rpsL | 781754 | c.195G>C | synonymous_variant | 0.14 |
rpsL | 781760 | c.201T>C | synonymous_variant | 0.13 |
rpsL | 781772 | c.213C>A | synonymous_variant | 0.12 |
rpsL | 781808 | c.249C>T | synonymous_variant | 0.15 |
rpsL | 781811 | c.252C>T | synonymous_variant | 0.14 |
rplC | 800612 | c.-197A>G | upstream_gene_variant | 0.12 |
rplC | 800618 | c.-191T>C | upstream_gene_variant | 0.12 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472969 | n.1124A>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472970 | n.1125C>G | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473105 | n.1260G>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1473756 | n.99G>A | non_coding_transcript_exon_variant | 0.17 |
rrl | 1473758 | n.101G>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1473945 | n.288T>A | non_coding_transcript_exon_variant | 0.21 |
rrl | 1473946 | n.289A>T | non_coding_transcript_exon_variant | 0.21 |
rrl | 1474093 | n.436G>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474099 | n.442G>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474103 | n.446A>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474181 | n.524C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474249 | n.592G>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1474794 | n.1137C>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1474823 | n.1166C>T | non_coding_transcript_exon_variant | 0.22 |
rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475088 | n.1431A>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475199 | n.1542G>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475206 | n.1549C>T | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475209 | n.1552G>C | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475213 | n.1556C>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1475355 | n.1698C>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475369 | n.1712G>T | non_coding_transcript_exon_variant | 0.17 |
rrl | 1475402 | n.1745C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475429 | n.1772G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475436 | n.1779C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475483 | n.1826C>T | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.16 |
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.13 |
rrl | 1475599 | n.1942A>G | non_coding_transcript_exon_variant | 0.15 |
rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 0.18 |
rrl | 1475657 | n.2000A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475659 | n.2002G>T | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475765 | n.2111delG | non_coding_transcript_exon_variant | 0.23 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.13 |
rrl | 1476214 | n.2557G>A | 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 |
katG | 2155678 | p.Arg145Leu | missense_variant | 0.99 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2168757 | p.Gln619Arg | missense_variant | 1.0 |
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 | 3877949 | p.Thr187Ala | missense_variant | 0.96 |
rpoA | 3878436 | c.72A>G | synonymous_variant | 0.12 |
rpoA | 3878442 | c.66G>C | synonymous_variant | 0.12 |
clpC1 | 4038860 | c.1845G>C | synonymous_variant | 0.12 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4245725 | c.-789A>G | upstream_gene_variant | 0.14 |
embB | 4245726 | c.-788T>C | upstream_gene_variant | 0.14 |
embB | 4245737 | c.-777A>C | upstream_gene_variant | 0.13 |
embB | 4245740 | c.-774T>C | upstream_gene_variant | 0.13 |
embB | 4247491 | c.978G>C | synonymous_variant | 0.12 |
embB | 4247539 | c.1026T>C | synonymous_variant | 0.12 |
embB | 4248157 | c.1644A>G | synonymous_variant | 0.12 |
embB | 4248304 | c.1791G>C | synonymous_variant | 0.14 |
embB | 4248316 | c.1803C>G | synonymous_variant | 0.12 |
embB | 4248319 | c.1806A>G | synonymous_variant | 0.13 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.96 |
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 |