This reports the protocol used to align the RiceRufipogon_BACend_OMAP features to tigrv4-genome. Fri Apr 14 15:29:46 2006 Source of RiceRufipogon_BACend_OMAP : from Gramene markers database, originally From genbank Nucleotide database with keyword 'OR_CBa' Alignment procedure details --------------------------- 70982 RiceRufipogon_BACend_OMAP are aligned to tigrv4-genome 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 : 150483 # unique Features these alignments represent: 69141 % of total features these alignments represent : 97.41 % Following is the GAP distribution Gaps # alignments -------- -------- 0 82651 1 20406 2 8061 3 4337 4 2609 5 2091 6 1816 7 1558 8 1110 9 880 10 801 20 4682 30 2123 40 1090 50 992 60 537 70 508 80 280 90 220 100 157 200 1730 300 860 400 624 500 478 600 177 700 106 800 143 900 68 10000 2175 Features with gaps > 40 bp are deleted # remaining Alignments : 134215 # unique Features these remaining alignments represent: 62451 % of total features these alignments represent : 87.98 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 0 29 76 39 186 49 238 59 465 69 627 79 667 89 1664 90 564 91 626 92 930 93 1369 94 2026 95 3508 96 7269 97 12415 98 19306 99 36000 100 46279 Features less than 90 % coverage are deleted. # remaining Alignments : 129734 # unique Features these remaining alignments represent: 59611 % of total features these alignments represent : 83.98 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 89 91 203 92 357 93 711 94 1618 95 4902 96 10414 97 16343 98 34663 99 55047 100 5387 Features less than 92 % identity are deleted. # remaining Alignments : 129442 # unique Features these remaining alignments represent: 59484 % of total features these alignments represent : 83.80 % Frequency distribution of the remaining features # hits # features -------- -------- 1 49768 2 2303 3 1468 4 1232 5 806 6 516 8 1331 9 248 10 248 20 844 30 257 40 203 50 82 100 130 Features that hit more than thrice are deleted. # remaining Alignments : 58778 # unique Features these remaining alignments represent: 53539 % of total features these alignments represent : 75.43 %