Marker Annotation Report
This analysis shows the results of using BLAST to match the markers sequence in the T3 database to the the wheat genome sequence.The BLAST results link to GBrowse URGI and Ensembl genome browsers. The top level page gives a summary of the matching markers for each experiment.
Select the match link to view the BLAST hits for each experiment.
Methods: A marker is identified as a match if either
1. the sequence homology is > 99% and aligment length is > 95% of the query sequence.
2. there is only one mismatch and the alignment length is > 95% of the query sequence.
The analysis uses blastn v2.2.28+ with the following arguments "-outfmt 6 -dust no -word_size 16 -task megablast -evalue 1e-08".
| Experiment | total markers | OatHulless | OatSeedRef100 | OatSeedRef90 |
| POGI_2019 | 240958 | 15153 (6%) | 3371 (1%) | 3215 (1%) |
| CornellMetabolomics_2016 | 239424 | 15121 (6%) | 3363 (1%) | 3206 (1%) |
| SDSU_2017_GBS | 239667 | 15122 (6%) | 3363 (1%) | 3206 (1%) |
| POGI_2017 | 239612 | 15120 (6%) | 3363 (1%) | 3206 (1%) |
| CornellMetabolomics_2014 | 81998 | 4942 (6%) | 1138 (1%) | 1076 (1%) |
| POGI_2015_UOPN | 241212 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| POGI_2015_Other | 241215 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| POGI_2015_SOAP | 241209 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| POGI_2015_ENCORE | 241209 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| POGI_2015_UMN | 241210 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| POGI_2015_UWM | 241210 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| POGI_2015_UIL | 241212 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| POGI_2015_SDSU | 241211 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| POGI_2015_Aberdeen | 241212 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| POGI_2015_UCDavis | 241212 | 15181 (6%) | 3381 (1%) | 3224 (1%) |
| NSGC_2014_Infinium | 3776 | 2786 (74%) | 2187 (58%) | 2016 (53%) |
| Oliver_2013_CDC_SOL-FI/HIFI | 458 | 343 (75%) | 289 (63%) | 268 (59%) |
| Oliver_2013_PROVENA/GS-7 | 412 | 326 (79%) | 260 (63%) | 246 (60%) |
| Oliver_2013_OGLE/TAMO301 | 821 | 632 (77%) | 537 (65%) | 495 (60%) |
| Oliver_2013_OTANA/PI260616 | 475 | 370 (78%) | 292 (61%) | 273 (57%) |
| Oliver_2013_KANOTA/OGLE | 1418 | 1134 (80%) | 922 (65%) | 856 (60%) |
| Oliver_2013_HURDAL/Z-595-7 | 453 | 364 (80%) | 304 (67%) | 282 (62%) |
| CORE_2014_GBS | 2635 | 383 (15%) | 115 (4%) | 106 (4%) |
| CORE_2010_Infinium | 1932 | 1487 (77%) | 1222 (63%) | 1115 (58%) |