This reports the protocol used to align the Rice_FSTtos17 features to tigrv4-genome. Fri Apr 14 11:57:14 2006 Source of Rice_FSTtos17 : from Gramene markers database, originally Downloaded from genbank using the query 'txid4530[orgn] AND tos17[TITL] AND GSS[KYWD]' Alignment procedure details --------------------------- 18024 Rice_FSTtos17 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 : 18366 # unique Features these alignments represent: 17908 % of total features these alignments represent : 99.36 % Following is the GAP distribution Gaps # alignments -------- -------- 0 14264 1 1477 2 686 3 477 4 230 5 158 6 145 7 105 8 83 9 69 10 71 20 281 30 98 40 47 50 21 60 14 70 8 80 5 90 3 100 9 200 30 300 21 400 27 500 26 600 0 700 0 800 0 900 0 10000 8 Features with gaps > 40 bp are deleted # remaining Alignments : 18191 # unique Features these remaining alignments represent: 17746 % of total features these alignments represent : 98.46 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 0 29 0 39 5 49 12 59 53 69 53 79 217 89 794 90 168 91 186 92 233 93 316 94 367 95 500 96 699 97 943 98 1563 99 2460 100 9622 Features less than 90 % coverage are deleted. # remaining Alignments : 16897 # unique Features these remaining alignments represent: 16503 % of total features these alignments represent : 91.56 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 2 94 1 95 3 96 19 97 70 98 459 99 4953 100 11390 Features less than 92 % identity are deleted. # remaining Alignments : 16897 # unique Features these remaining alignments represent: 16503 % of total features these alignments represent : 91.56 % Frequency distribution of the remaining features # hits # features -------- -------- 1 16163 2 295 3 42 4 2 5 0 6 0 8 0 9 0 10 1 20 0 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 16879 # unique Features these remaining alignments represent: 16500 % of total features these alignments represent : 91.54 %