This reports the protocol used to align the Maize_MethylFilter_CSHL features to Maize_BACs_20060126. Mon Feb 13 23:45:35 2006 Source of Maize_MethylFilter_CSHL : Methyl-filtered CSHL maize sequence, downloaded from genbank with query '(txid4577[ORGN] AND McCombie[AUTH] AND methyl[TITL] AND 2002[MDAT])' Alignment procedure details --------------------------- 66390 Maize_MethylFilter_CSHL 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 : 49122 # unique Features these alignments represent: 22707 % of total features these alignments represent : 34.20 % Following is the Gap distribution Gaps # alignments -------- -------- 0 19689 1 6166 2 2689 3 1566 4 1038 5 836 6 707 7 559 8 539 9 530 10 394 20 2263 30 1060 40 663 50 474 60 269 70 247 80 165 90 148 100 137 200 940 300 381 400 338 500 239 600 139 700 50 800 90 900 88 10000 2265 Features with gaps > 40 bp are deleted # remaining Alignments : 38699 # unique Features these remaining alignments represent: 18742 % of total features these alignments represent : 28.23 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 0 29 230 39 576 49 569 59 604 69 668 79 708 89 1820 90 637 91 968 92 1312 93 1568 94 2403 95 2928 96 3749 97 4495 98 5251 99 4662 100 5551 Features less than 90 % coverage are deleted. # remaining Alignments : 32914 # unique Features these remaining alignments represent: 14974 % of total features these alignments represent : 22.55 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 344 91 569 92 1014 93 1685 94 2468 95 3545 96 4753 97 5749 98 5522 99 4555 100 2710 Features less than 92 % identity are deleted. # remaining Alignments : 32001 # unique Features these remaining alignments represent: 14491 % of total features these alignments represent : 21.83 % Frequency distribution of the remaining features # hits # features -------- -------- 1 8309 2 2724 3 1234 4 733 5 453 6 321 8 344 9 97 10 59 20 184 30 24 40 5 50 1 100 3 Features that hit more than thrice are deleted. # remaining Alignments : 17459 # unique Features these remaining alignments represent: 12267 % of total features these alignments represent : 18.48 %