Run ID: SRR12416829
Sample name:
Date: 03-04-2023 06:48:05
Number of reads: 5484039
Percentage reads mapped: 90.49
Strain: lineage2.2.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage2 | East-Asian | Beijing | RD105 | 0.99 |
lineage2.2 | East-Asian (Beijing) | Beijing-RD207 | RD105;RD207 | 0.99 |
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 | 0.91 | rifampicin |
rpoC | 764841 | p.Ile491Thr | missense_variant | 0.86 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.93 | streptomycin |
fabG1 | 1673423 | c.-17G>T | upstream_gene_variant | 0.99 | isoniazid, ethionamide |
katG | 2155732 | p.Gln127Pro | missense_variant | 0.97 | isoniazid |
pncA | 2289252 | c.-11A>G | upstream_gene_variant | 1.0 | pyrazinamide |
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 | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.98 |
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 |
rpoB | 760223 | c.417T>C | synonymous_variant | 0.15 |
rpoB | 760235 | c.429T>C | synonymous_variant | 0.15 |
rpoB | 760283 | c.477G>C | synonymous_variant | 0.14 |
rpoB | 760298 | c.492G>C | synonymous_variant | 0.14 |
rpoB | 760328 | c.522G>C | synonymous_variant | 0.13 |
rpoB | 761015 | c.1209G>C | synonymous_variant | 0.14 |
rpoB | 761021 | c.1215G>C | synonymous_variant | 0.13 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 764858 | c.1489T>C | synonymous_variant | 0.15 |
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 |
fbiC | 1302874 | c.-57G>A | upstream_gene_variant | 0.18 |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrl | 1475599 | n.1942A>G | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 0.14 |
rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 0.13 |
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 | 1476214 | n.2557G>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.14 |
rpsA | 1833410 | c.-132G>A | upstream_gene_variant | 1.0 |
rpsA | 1833940 | c.399C>G | synonymous_variant | 0.14 |
rpsA | 1834012 | c.471G>C | synonymous_variant | 0.15 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 |
rpsA | 1834465 | c.924T>C | synonymous_variant | 0.13 |
rpsA | 1834468 | c.927A>G | synonymous_variant | 0.13 |
rpsA | 1834489 | c.948T>C | synonymous_variant | 0.13 |
rpsA | 1834495 | c.954G>A | synonymous_variant | 0.13 |
rpsA | 1834499 | c.958C>T | synonymous_variant | 0.14 |
rpsA | 1834528 | c.987T>C | synonymous_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.99 |
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 |
kasA | 2519206 | c.1092C>T | synonymous_variant | 0.13 |
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 |
alr | 3841614 | c.-194C>G | upstream_gene_variant | 1.0 |
rpoA | 3878076 | c.432C>T | synonymous_variant | 0.13 |
rpoA | 3878094 | c.414C>G | synonymous_variant | 0.14 |
rpoA | 3878103 | c.405A>G | synonymous_variant | 0.15 |
rpoA | 3878106 | c.402G>C | synonymous_variant | 0.14 |
rpoA | 3878193 | c.315T>C | synonymous_variant | 0.13 |
rpoA | 3878205 | c.303T>C | synonymous_variant | 0.14 |
rpoA | 3878217 | c.291A>G | synonymous_variant | 0.16 |
rpoA | 3878232 | c.276G>C | synonymous_variant | 0.13 |
rpoA | 3878247 | c.261G>C | synonymous_variant | 0.15 |
rpoA | 3878271 | c.237T>C | synonymous_variant | 0.14 |
rpoA | 3878276 | c.232C>T | synonymous_variant | 0.14 |
rpoA | 3878284 | p.Glu75Ala | missense_variant | 0.13 |
rpoA | 3878292 | c.216T>C | synonymous_variant | 0.15 |
rpoA | 3878304 | c.204G>C | synonymous_variant | 0.16 |
rpoA | 3878313 | c.195G>T | synonymous_variant | 0.16 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243460 | c.228C>T | synonymous_variant | 0.99 |
embB | 4248220 | c.1707A>C | synonymous_variant | 0.13 |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.99 |
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 |