This reports the protocol used to align the RiceIndica_EST_BGI features to tigrv4-genome. Fri Apr 14 12:01:39 2006 Source of RiceIndica_EST_BGI : Oryza indica ESTs from Gramene markers database, originally downloaded from http://btn.genomics.org.cn/ Alignment procedure details --------------------------- 85719 RiceIndica_EST_BGI are aligned to tigrv4-genome using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets. Initial summary # alignments : 86501 # unique Features these alignments represent: 81219 % of total features these alignments represent : 94.75 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 0 19 0 29 18 39 109 49 151 59 361 69 470 79 739 89 2796 90 725 91 782 92 979 93 1183 94 1579 95 2302 96 3171 97 4536 98 7226 99 14384 100 44990 Alignments less than 95 % coverage are deleted # remaining Alignments : 74365 # unique Features these remaining alignments represent: 69808 % of total features these alignments represent : 81.44 % GAP distribution of the remaining features Gaps # alignments -------- -------- 1000 62173 2000 8939 3000 2053 4000 663 5000 190 6000 90 7000 71 8000 42 9000 26 10000 13 20000 79 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 73828 # unique Features these remaining alignments represent: 69307 % of total features these alignments represent : 80.85 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 11 95 143 96 513 97 1872 98 7994 99 35638 100 27657 Frequency distribution of the remaining features # hits # features -------- -------- 1 67848 2 730 3 241 4 87 5 50 6 74 8 208 9 41 10 9 20 11 30 1 40 1 50 3 100 2 Features that hit more than four times are deleted. # remaining Alignments : 70379 # unique Features these remaining alignments represent: 68906 % of total features these alignments represent : 80.39 %