This reports the protocol used to align the RiceIndica_ESTcluster_BGI features to tigrv4-genome. Fri Apr 14 11:58:11 2006 Source of RiceIndica_ESTcluster_BGI : Oryza indica clusters from Gramene markers database, originally downloaded from http://btn.genomics.org.cn/ Alignment procedure details --------------------------- 23559 RiceIndica_ESTcluster_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 : 23444 # unique Features these alignments represent: 22410 % of total features these alignments represent : 95.12 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 0 19 0 29 4 39 23 49 53 59 144 69 184 79 286 89 465 90 79 91 110 92 128 93 143 94 190 95 283 96 379 97 620 98 1270 99 2959 100 16124 Alignments less than 95 % coverage are deleted # remaining Alignments : 21359 # unique Features these remaining alignments represent: 20552 % of total features these alignments represent : 87.24 % GAP distribution of the remaining features Gaps # alignments -------- -------- 1000 16069 2000 3116 3000 1264 4000 478 5000 185 6000 82 7000 48 8000 27 9000 19 10000 13 20000 27 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 20927 # unique Features these remaining alignments represent: 20145 % of total features these alignments represent : 85.51 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 2 95 37 96 140 97 504 98 1810 99 10916 100 7518 Frequency distribution of the remaining features # hits # features -------- -------- 1 19850 2 215 3 29 4 14 5 6 6 12 8 9 9 2 10 0 20 2 30 1 40 2 50 1 100 2 Features that hit more than four times are deleted. # remaining Alignments : 20423 # unique Features these remaining alignments represent: 20108 % of total features these alignments represent : 85.35 %