Run ID: SRR14782555
Sample name:
Date: 03-04-2023 11:30:24
Number of reads: 622862
Percentage reads mapped: 25.35
Strain: lineage2.2.1
Drug-resistance: Pre-XDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.98 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.96 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 1.0 | ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin |
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.95 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288778 | p.Val155Gly | missense_variant | 0.9 | pyrazinamide |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid |
thyA | 3073808 | p.Arg222Gly | missense_variant | 1.0 | para-aminosalicylic_acid |
embB | 4247431 | p.Met306Ile | 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 |
gyrA | 9647 | c.2346C>G | synonymous_variant | 0.14 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575156 | c.-192G>A | upstream_gene_variant | 0.25 |
mshA | 575248 | c.-100C>A | upstream_gene_variant | 0.13 |
mshA | 575460 | p.Val38Ala | missense_variant | 0.12 |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 |
mshA | 576446 | p.Thr367Pro | missense_variant | 0.33 |
mshA | 576496 | p.Asp383Glu | missense_variant | 0.22 |
mshA | 576616 | c.1269G>C | synonymous_variant | 0.6 |
ccsA | 620625 | p.Ile245Met | missense_variant | 0.79 |
rpoB | 761268 | p.Ile488Val | missense_variant | 0.92 |
rpoB | 761470 | p.Val555Gly | missense_variant | 0.2 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
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 |
mmpL5 | 777883 | p.Gly200Arg | missense_variant | 0.27 |
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 | 0.91 |
embR | 1416435 | p.Ala305Pro | missense_variant | 0.23 |
atpE | 1461235 | p.Tyr64Phe | missense_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472108 | n.263C>A | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472127 | n.282C>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472128 | n.283G>C | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472129 | n.284G>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472135 | n.290C>G | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472151 | n.306C>T | non_coding_transcript_exon_variant | 0.32 |
rrs | 1472153 | n.308G>C | non_coding_transcript_exon_variant | 0.3 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.44 |
rrs | 1472223 | n.378C>G | non_coding_transcript_exon_variant | 0.22 |
rrs | 1472228 | n.383G>C | non_coding_transcript_exon_variant | 0.13 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472607 | n.762G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472708 | n.863T>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.53 |
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.54 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.52 |
rrs | 1472887 | n.1042G>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473020 | n.1175T>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.21 |
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.26 |
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.16 |
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.15 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.19 |
rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.22 |
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.24 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.2 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.28 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.28 |
rrl | 1475870 | n.2213G>A | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475874 | n.2217C>T | non_coding_transcript_exon_variant | 0.18 |
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.61 |
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.64 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.79 |
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.78 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.79 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.81 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.82 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.84 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.84 |
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.84 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.82 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.84 |
rrl | 1476411 | n.2754G>T | non_coding_transcript_exon_variant | 0.84 |
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.85 |
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.87 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.87 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476463 | n.2806C>A | non_coding_transcript_exon_variant | 0.89 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.29 |
fabG1 | 1673553 | p.Asp38Glu | missense_variant | 0.62 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102535 | c.508C>T | synonymous_variant | 0.11 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289709 | c.-468G>T | upstream_gene_variant | 0.18 |
folC | 2747459 | p.Leu47Pro | missense_variant | 0.2 |
pepQ | 2859918 | c.501A>C | synonymous_variant | 0.22 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568428 | c.252A>G | synonymous_variant | 1.0 |
Rv3236c | 3612537 | p.Gly194Trp | missense_variant | 0.25 |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.9 |
fbiB | 3641810 | c.276G>C | synonymous_variant | 1.0 |
clpC1 | 4040244 | p.Gly154Ala | missense_variant | 0.2 |
embC | 4240409 | p.Pro183Ala | missense_variant | 0.67 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4247016 | p.Ser168Trp | missense_variant | 0.25 |
embB | 4247020 | c.507C>G | synonymous_variant | 0.6 |
embB | 4248189 | p.Arg559Gln | missense_variant | 0.14 |
embB | 4248324 | p.Ala604Gly | missense_variant | 0.25 |
embB | 4248328 | c.1815G>C | synonymous_variant | 0.38 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.93 |
aftB | 4267649 | c.1188T>G | synonymous_variant | 0.21 |
ethA | 4326339 | p.Asn379Asp | 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 | 0.93 |
gid | 4408093 | p.Gly37Ala | missense_variant | 0.25 |