From: Flexible and scalable genotyping-by-sequencing strategies for population studies
MlyI | AluI | RsaI | DraI | EcoRV | StuI | HaeIII | HincII | |
---|---|---|---|---|---|---|---|---|
Maize | ||||||||
Total predicted sites | 3,326,697 | 8,886,974 | 4,870,173 | 894,567 | 427,268 | 515,556 | 7,667,926 | 1,376,427 |
Predicted sites 100-1000 bp | 1,898,039 | 5,083,913 | 3,105,315 | 320,985 | 71,742 | 134,944 | 3,823,749 | 583,683 |
Predicted sites 100-400 bp | 1,010,023 | 3,701,470 | 1,815,078 | 175,669 | 23,107 | 69,468 | 2,690,200 | 246,190 |
Predicted sites 100-200 bp | 391,160 | 1,936,120 | 746,075 | 78,672 | 10,382 | 21,045 | 1,436,751 | 103,861 |
Total predicted sites covered* | 0.2226 | 0.2350 | 0.1705 | 0.1514 | 0.0604 | 0.0818 | 0.2684 | 0.0504 |
Covered sites 100-1000 bp* | 0.3529 | 0.3465 | 0.2301 | 0.3701 | 0.3365 | 0.2986 | 0.4550 | 0.1068 |
Covered sites 100-400 bp* | 0.5756 | 0.4721 | 0.3877 | 0.6503 | 0.7259 | 0.4126 | 0.6296 | 0.2439 |
Covered sites 100-200 bp* | 0.5986 | 0.5589 | 0.5524 | 0.7354 | 0.6872 | 0.4372 | 0.6746 | 0.2884 |
Fraction of MQ 20 reads aligning to predicted sites | 0.8363 | 0.8090 | 0.9000 | 0.9485 | 0.8373 | 0.8810 | 0.8874 | 0.8147 |
Rice | ||||||||
Total predicted sites | 371,222 | 1,486,508 | 1,037,100 | 301,435 | 78,181 | 60,707 | 1,204,615 | 260,304 |
Predicted sites 100-1000 bp | 188,264 | 875,739 | 641,398 | 128,513 | 14,728 | 10,684 | 565,466 | 111,036 |
Predicted sites 100-400 bp | 90,536 | 623,512 | 408,979 | 70,456 | 6,146 | 4,093 | 371,004 | 49,065 |
Predicted sites 100-200 bp | 37,870 | 308,092 | 183,142 | 32,571 | 2,145 | 1,175 | 188,652 | 19,823 |
Total predicted sites covered* | 0.2150 | 0.5132 | 0.4420 | 0.3281 | 0.1224 | 0.0867 | 0.4048 | 0.1757 |
Covered sites 100-1000 bp* | 0.3578 | 0.7423 | 0.6226 | 0.6715 | 0.6005 | 0.4536 | 0.7235 | 0.3819 |
Covered sites 100-400 bp* | 0.7026 | 0.8692 | 0.8513 | 0.9136 | 0.8967 | 0.6426 | 0.8732 | 0.5978 |
Covered sites 100-200 bp* | 0.8202 | 0.8684 | 0.8575 | 0.9062 | 0.9152 | 0.7668 | 0.8606 | 0.5681 |
Fraction of MQ 20 reads aligning to predicted sites | 0.7138 | 0.9224 | 0.9457 | 0.9854 | 0.9138 | 0.9361 | 0.9484 | 0.8298 |