This reports the protocol used to align the Maize_tug features to Maize_BACs. Kiran Ratnapu Tue Mar 29 17:16:06 2005 Source of Maize_tug : Downloaded from :http://www.plantgdb.org/download//PlantTUGs/ZMtug.gz Alignment procedure details --------------------------- 71655 Maize_tug are aligned to Maize_BACs using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets. Initial summary # alignments : 7366 # unique Features these alignments represent: 4890 % of total features these alignments represent : 6.82 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 0 19 15 29 199 39 389 49 433 59 448 69 392 79 551 89 901 90 151 91 171 92 236 93 255 94 307 95 405 96 460 97 544 98 498 99 489 100 522 Alignments less than 95 % coverage are deleted # remaining Alignments : 2518 # unique Features these remaining alignments represent: 1612 % of total features these alignments represent : 2.25 % RICE_GAP distribution of the remaining features Rice_Gaps # alignments -------- -------- 1000 2318 2000 94 3000 44 4000 16 5000 6 6000 5 7000 5 8000 1 9000 5 10000 5 20000 9 Alignments with gaps on rice > 4000 bp are deleted # remaining Alignments : 2472 # unique Features these remaining alignments represent: 1582 % of total features these alignments represent : 2.21 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 22 95 142 96 309 97 383 98 650 99 569 100 397 Frequency distribution of the remaining features # hits # features -------- -------- 1 1193 2 239 3 56 4 36 5 21 6 7 8 12 9 5 10 3 20 8 30 1 40 0 50 1 100 0 Features that hit more than four times are deleted. # remaining Alignments : 1983 # unique Features these remaining alignments represent: 1524 % of total features these alignments represent : 2.13 %