This reports the protocol used to align the Maize_HiCotCluster_TIGR features to Maize_BACs_20060126. Mon Feb 13 23:43:18 2006 Source of Maize_HiCotCluster_TIGR : Downloaded from TIGR using the link ftp://ftp.tigr.org/pub/data/MAIZE/AZMs/release_4.0/zmg_fasta.4.0HC_022304.gz Alignment procedure details --------------------------- 172600 Maize_HiCotCluster_TIGR 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 # alignments : 64807 # unique Features these alignments represent: 42251 % of total features these alignments represent : 24.48 % Following is the Gap distribution Gaps # alignments -------- -------- 0 20508 1 7632 2 3322 3 1998 4 1428 5 1168 6 1026 7 1018 8 827 9 706 10 728 20 4780 30 2568 40 1583 50 1182 60 985 70 692 80 590 90 481 100 455 200 2596 300 1050 400 722 500 447 600 197 700 143 800 110 900 85 10000 1989 Features with gaps > 40 bp are deleted # remaining Alignments : 49292 # unique Features these remaining alignments represent: 31335 % of total features these alignments represent : 18.15 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 916 19 4693 29 5092 39 3760 49 2648 59 2028 69 1753 79 1535 89 2390 90 511 91 656 92 807 93 1023 94 1206 95 1422 96 1895 97 2348 98 2699 99 2841 100 9069 Features less than 90 % coverage are deleted. # remaining Alignments : 23979 # unique Features these remaining alignments represent: 13604 % of total features these alignments represent : 7.88 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 295 91 379 92 611 93 1051 94 1316 95 1812 96 2418 97 2868 98 2972 99 6556 100 3701 Features less than 92 % identity are deleted. # remaining Alignments : 23305 # unique Features these remaining alignments represent: 13159 % of total features these alignments represent : 7.62 % Frequency distribution of the remaining features # hits # features -------- -------- 1 9259 2 2090 3 722 4 330 5 212 6 176 8 156 9 45 10 38 20 111 30 7 40 6 50 2 100 5 Features that hit more than thrice are deleted. # remaining Alignments : 15605 # unique Features these remaining alignments represent: 12071 % of total features these alignments represent : 6.99 %