This reports the protocol used to align the Maize_MethylFilter_Orion features to Maize_BACs_20060126. Tue Feb 14 00:28:19 2006 Source of Maize_MethylFilter_Orion : Methyl-filtered TIGR maize sequence, downloaded from genbank with query '(txid4577[ORGN] AND Quackenbush[AUTH] AND "methylation"[ALL] )' Alignment procedure details --------------------------- 450197 Maize_MethylFilter_Orion 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 : 280340 # unique Features these alignments represent: 120426 % of total features these alignments represent : 26.75 % Following is the Gap distribution Gaps # alignments -------- -------- 0 99083 1 35198 2 16553 3 10375 4 6747 5 5176 6 4487 7 3750 8 3220 9 2899 10 2498 20 14237 30 6823 40 3670 50 2556 60 2321 70 1638 80 1169 90 1066 100 978 200 6141 300 2771 400 1868 500 1257 600 614 700 347 800 326 900 408 10000 11426 Features with gaps > 40 bp are deleted # remaining Alignments : 214716 # unique Features these remaining alignments represent: 93630 % of total features these alignments represent : 20.80 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 175 29 4388 39 4361 49 3362 59 2942 69 2795 79 3076 89 6330 90 2303 91 3431 92 4922 93 6699 94 9676 95 14138 96 19490 97 26050 98 29401 99 28043 100 43134 Features less than 90 % coverage are deleted. # remaining Alignments : 185036 # unique Features these remaining alignments represent: 75080 % of total features these alignments represent : 16.68 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 1313 91 2403 92 4266 93 7301 94 12454 95 18880 96 27018 97 31271 98 30953 99 28565 100 20612 Features less than 92 % identity are deleted. # remaining Alignments : 181320 # unique Features these remaining alignments represent: 72991 % of total features these alignments represent : 16.21 % Frequency distribution of the remaining features # hits # features -------- -------- 1 39454 2 13903 3 6639 4 3971 5 2552 6 1676 8 2055 9 567 10 461 20 1402 30 186 40 61 50 24 100 36 Features that hit more than thrice are deleted. # remaining Alignments : 87177 # unique Features these remaining alignments represent: 59996 % of total features these alignments represent : 13.33 %