This reports the protocol used to align the Rice_FST-TDNA features to tigrv4-genome. Fri Apr 14 11:56:05 2006 Source of Rice_FST-TDNA : from Gramene markers database, originally Downloaded from Genbank with query "txid4530[orgn] AND GSS[PROP] AND T-DNA insertion lines" Alignment procedure details --------------------------- 14533 Rice_FST-TDNA 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 : 17906 # unique Features these alignments represent: 13906 % of total features these alignments represent : 95.69 % Following is the GAP distribution Gaps # alignments -------- -------- 0 16507 1 363 2 167 3 51 4 27 5 25 6 36 7 23 8 25 9 17 10 13 20 93 30 57 40 48 50 33 60 24 70 19 80 22 90 18 100 12 200 62 300 35 400 42 500 23 600 0 700 0 800 1 900 2 10000 68 Features with gaps > 40 bp are deleted # remaining Alignments : 17452 # unique Features these remaining alignments represent: 13622 % of total features these alignments represent : 93.73 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 0 29 1 39 5 49 24 59 91 69 134 79 173 89 536 90 89 91 100 92 166 93 154 94 527 95 278 96 436 97 646 98 998 99 1364 100 11730 Features less than 90 % coverage are deleted. # remaining Alignments : 16403 # unique Features these remaining alignments represent: 12714 % of total features these alignments represent : 87.48 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 28 91 30 92 28 93 50 94 72 95 118 96 276 97 716 98 1101 99 3226 100 10758 Features less than 92 % identity are deleted. # remaining Alignments : 16345 # unique Features these remaining alignments represent: 12668 % of total features these alignments represent : 87.17 % Frequency distribution of the remaining features # hits # features -------- -------- 1 12363 2 127 3 34 4 33 5 33 6 18 8 11 9 4 10 3 20 11 30 11 40 1 50 2 100 9 Features that hit more than thrice are deleted. # remaining Alignments : 12719 # unique Features these remaining alignments represent: 12524 % of total features these alignments represent : 86.18 %