This reports the protocol used to align the Rice_MarkerRFLP features to tigrv4-genome. Fri Apr 14 11:50:31 2006 Source of Rice_MarkerRFLP : Obtained from Gramene Marker database Alignment procedure details --------------------------- 4333 Rice_MarkerRFLP 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 : 4377 # unique Features these alignments represent: 4252 % of total features these alignments represent : 98.13 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 0 19 0 29 0 39 3 49 5 59 23 69 76 79 165 89 392 90 71 91 108 92 159 93 172 94 218 95 297 96 406 97 465 98 362 99 471 100 984 Alignments less than 95 % coverage are deleted # remaining Alignments : 2693 # unique Features these remaining alignments represent: 2594 % of total features these alignments represent : 59.87 % GAP distribution of the remaining features Gaps # alignments -------- -------- 1000 2316 2000 263 3000 72 4000 26 5000 5 6000 4 7000 4 8000 1 9000 1 10000 0 20000 1 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 2677 # unique Features these remaining alignments represent: 2579 % of total features these alignments represent : 59.52 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 0 95 1 96 8 97 25 98 160 99 1066 100 1417 Frequency distribution of the remaining features # hits # features -------- -------- 1 2518 2 46 3 7 4 1 5 4 6 0 8 3 9 0 10 0 20 0 30 0 40 0 50 0 100 0 Features that hit more than four times are deleted. # remaining Alignments : 2635 # unique Features these remaining alignments represent: 2572 % of total features these alignments represent : 59.36 %