This reports the protocol used to align the Maize_BACend features to Maize_BACs_20060126. Sat Feb 18 22:26:23 2006 Source of Maize_BACend : Downloaded from genbank with query '(txid4577[orgn] AND Wing[AUTH] AND Messing[AUTH] AND "BAC ends"[ALL])' Alignment procedure details --------------------------- 472700 Maize_BACend are aligned to Maize_BACs_20060126 using blat with blat parameters -minScore=160 followed by PslReps with -minAli=0.90 -nearTop=0.01 -singleHit. This was followed by a filtering procedure described below and applied in general to 'Same Species Genomic' data sets. Initial summary # aligments : 884902 # unique Features these alignments represent: 333324 % of total features these alignments represent : 70.51 % Following is the Gap distribution Gaps # alignments -------- -------- 0 219096 1 43772 2 22432 3 17153 4 15391 5 15160 6 16187 7 15488 8 14377 9 13735 10 13253 20 109994 30 94080 40 64312 50 36872 60 22700 70 14683 80 9426 90 6599 100 4701 200 18221 300 7620 400 4797 500 3644 600 1109 700 753 800 567 900 766 10000 18578 Features with gaps > 40 bp are deleted # remaining Aligments : 674430 # unique Features these represent alignments represent: 245030 % of total features these alignments represent : 51.84 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 93 29 3217 39 5270 49 4986 59 7766 69 18024 79 42453 89 119919 90 27456 91 33310 92 40013 93 44711 94 49446 95 54450 96 58632 97 58046 98 50249 99 36661 100 19728 Features less than 90 % coverage are deleted. # remaining Aligments : 445911 # unique Features these represent alignments represent: 145898 % of total features these alignments represent : 30.86 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 4540 91 6704 92 13015 93 23550 94 40968 95 65303 96 84949 97 87339 98 77344 99 30503 100 11696 Features less than 92 % identity are deleted. # remaining Aligments : 434667 # unique Features these represent alignments represent: 140064 % of total features these alignments represent : 29.63 % Frequency distribution of the remaining features # hits # features -------- -------- 1 58615 2 29214 3 16178 4 10043 5 6934 6 5000 8 6068 9 1724 10 1289 20 4103 30 528 40 158 50 66 100 99 Features that hit more than thrice are deleted. # remaining Aligments : 165577 # unique Features these represent alignments represent: 104007 % of total features these alignments represent : 22.00 %