Run ID: SRR6485010
Sample name:
Date: 04-04-2023 15:00:36
Number of reads: 4989633
Percentage reads mapped: 97.48
Strain: lineage2.2.1
Drug-resistance: MDR-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 |
lineage2.2.1 | East-Asian (Beijing) | Beijing-RD181 | RD105;RD207;RD181 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.98 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.98 | isoniazid |
pncA | 2288924 | c.317delT | frameshift_variant | 1.0 | pyrazinamide, pyrazinamide |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.97 | ethambutol |
ethA | 4327480 | c.-7T>C | upstream_gene_variant | 1.0 | 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 | 491100 | c.318C>T | synonymous_variant | 0.13 |
fgd1 | 491106 | c.324T>C | synonymous_variant | 0.15 |
fgd1 | 491121 | c.339A>G | synonymous_variant | 0.15 |
fgd1 | 491130 | c.348C>G | synonymous_variant | 0.17 |
fgd1 | 491144 | p.Ala121Asp | missense_variant | 0.16 |
fgd1 | 491151 | c.369G>A | synonymous_variant | 0.15 |
fgd1 | 491173 | c.391C>A | synonymous_variant | 0.16 |
fgd1 | 491181 | c.399T>C | synonymous_variant | 0.12 |
fgd1 | 491184 | c.402A>G | synonymous_variant | 0.12 |
fgd1 | 491191 | p.Gly137Arg | missense_variant | 0.12 |
fgd1 | 491194 | c.412_414delCTAinsTTG | synonymous_variant | 0.12 |
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 | 760834 | p.His343Arg | missense_variant | 0.7 |
rpoB | 761570 | c.1764T>C | synonymous_variant | 0.11 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.97 |
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 |
rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.13 |
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.12 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.22 |
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 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.19 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.2 |
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 | 3878322 | c.186A>G | synonymous_variant | 0.11 |
rpoA | 3878376 | c.132G>C | synonymous_variant | 0.11 |
rpoA | 3878385 | c.123C>G | synonymous_variant | 0.11 |
rpoA | 3878391 | c.117T>C | synonymous_variant | 0.11 |
rpoA | 3878424 | c.84G>C | synonymous_variant | 0.11 |
rpoA | 3878436 | c.72A>G | synonymous_variant | 0.11 |
rpoA | 3878442 | c.66G>C | synonymous_variant | 0.11 |
rpoA | 3878454 | c.54A>C | synonymous_variant | 0.12 |
rpoA | 3878484 | c.24C>A | synonymous_variant | 0.13 |
rpoA | 3878490 | c.18C>A | synonymous_variant | 0.14 |
rpoA | 3878496 | c.12A>T | synonymous_variant | 0.15 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.17 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.22 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.24 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.24 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.13 |
embB | 4246567 | c.54G>T | synonymous_variant | 0.13 |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.28 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.98 |
whiB6 | 4338563 | c.-42G>T | upstream_gene_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 |