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Table 2 Predicted site counts and coverage

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
  1. *A read alignment with MQ ≥20 is required for a site to be considered “covered”.