This reports the protocol used to align the Maize_HiCotMethylFilterCluster_TIGR features to Maize_BACs_20060126. Mon Feb 13 23:57:16 2006 Source of Maize_HiCotMethylFilterCluster_TIGR : Downloaded from TIGR using the link ftp://ftp.tigr.org/pub/data/MAIZE/AZMs/release_4.0/zmg_fasta.4.0ALL_022304.gz Alignment procedure details --------------------------- 243807 Maize_HiCotMethylFilterCluster_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 : 224994 # unique Features these alignments represent: 103157 % of total features these alignments represent : 42.31 % Following is the Gap distribution Gaps # alignments -------- -------- 0 72935 1 25434 2 11783 3 7572 4 4952 5 4043 6 3459 7 3202 8 2675 9 2303 10 2154 20 13239 30 6881 40 3902 50 2889 60 2476 70 1757 80 1332 90 1185 100 1010 200 6267 300 2640 400 1886 500 1181 600 563 700 409 800 355 900 359 10000 9855 Features with gaps > 40 bp are deleted # remaining Alignments : 164534 # unique Features these remaining alignments represent: 74074 % of total features these alignments represent : 30.38 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 2784 19 6859 29 6122 39 4632 49 3630 59 3131 69 2995 79 2931 89 5937 90 1854 91 2718 92 3728 93 5062 94 7174 95 10134 96 14218 97 18420 98 20866 99 19147 100 22192 Features less than 90 % coverage are deleted. # remaining Alignments : 123698 # unique Features these remaining alignments represent: 47341 % of total features these alignments represent : 19.42 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 1157 91 1826 92 3225 93 5624 94 9136 95 13650 96 18865 97 22061 98 21565 99 17989 100 8600 Features less than 92 % identity are deleted. # remaining Alignments : 120715 # unique Features these remaining alignments represent: 45610 % of total features these alignments represent : 18.71 % Frequency distribution of the remaining features # hits # features -------- -------- 1 22926 2 9015 3 4633 4 2727 5 1770 6 1214 8 1418 9 394 10 327 20 961 30 128 40 47 50 17 100 30 Features that hit more than thrice are deleted. # remaining Alignments : 54855 # unique Features these remaining alignments represent: 36574 % of total features these alignments represent : 15.00 %