This reports the protocol used to align the RiceNivara_BACend_OMAP features to tigrv4-genome. Fri Apr 14 16:21:06 2006 Source of RiceNivara_BACend_OMAP : from Gramene markers database, originally From genbank Nucleotide database with keyword 'OR_BBa' Alignment procedure details --------------------------- 106124 RiceNivara_BACend_OMAP 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 : 233996 # unique Features these alignments represent: 102172 % of total features these alignments represent : 96.28 % Following is the GAP distribution Gaps # alignments -------- -------- 0 131361 1 30102 2 11079 3 6620 4 4453 5 3361 6 3200 7 2318 8 1731 9 1495 10 1490 20 6768 30 3242 40 1696 50 1252 60 897 70 719 80 561 90 308 100 315 200 2696 300 1270 400 904 500 670 600 249 700 177 800 291 900 137 10000 3270 Features with gaps > 40 bp are deleted # remaining Alignments : 208916 # unique Features these remaining alignments represent: 92267 % of total features these alignments represent : 86.94 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 0 29 103 39 304 49 284 59 607 69 836 79 1066 89 2916 90 860 91 1174 92 1600 93 2348 94 3630 95 6204 96 11921 97 22087 98 33159 99 54988 100 64829 Features less than 90 % coverage are deleted. # remaining Alignments : 201952 # unique Features these remaining alignments represent: 87742 % of total features these alignments represent : 82.68 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 135 91 324 92 647 93 1374 94 3204 95 7840 96 18060 97 28472 98 54071 99 79247 100 8578 Features less than 92 % identity are deleted. # remaining Alignments : 201493 # unique Features these remaining alignments represent: 87521 % of total features these alignments represent : 82.47 % Frequency distribution of the remaining features # hits # features -------- -------- 1 71370 2 3641 3 2404 4 2026 5 1423 6 900 8 2260 9 428 10 411 20 1484 30 491 40 328 50 127 100 161 Features that hit more than thrice are deleted. # remaining Alignments : 85864 # unique Features these remaining alignments represent: 77415 % of total features these alignments represent : 72.95 %