This reports the protocol used to align the sorghum_wgs features to tigrv4-genome. Thu Aug 10 11:32:26 2006 Source of sorghum_wgs : Downloaded from trace archive under the query SPECIES_CODE='SORGHUM BICOLOR' Alignment procedure details --------------------------- 6749814 sorghum_wgs are aligned to tigrv4-genome using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Genomic' data sets. Initial summary # aligments : 3561092 # unique Features these alignments represent: 2561132 % of total features these alignments represent : 37.94 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 1051724 150 474113 200 293229 250 229178 300 189089 350 158306 400 144863 450 126744 500 118610 550 108168 600 92785 650 81728 700 75494 750 81175 800 86617 10000 249269 Alignments with matches less than 100 bp are filtered # remaining Aligments : 2519454 # unique Features these represent alignments represent: 1744503 % of total features these alignments represent : 25.85 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 2239555 2000 17905 3000 4960 4000 2937 5000 1503 6000 1796 7000 2026 8000 3179 9000 1895 10000 1515 20000 9428 Alignments with gaps > 4000 bp are filtered # remaining Aligments : 2265357 # unique Features these represent alignments represent: 1554276 % of total features these alignments represent : 23.03 % Frequency distribution of the remaining features # hits # features -------- -------- 1 1276251 2 123267 3 28611 4 45580 5 31626 6 41411 8 4263 9 1059 10 798 20 1368 30 34 40 5 50 1 100 2 Features that hit more than thrice are deleted. # remaining Aligments : 1608618 # unique Features these represent alignments represent: 1428129 % of total features these alignments represent : 21.16 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 3 20 928 30 8310 40 39123 50 104748 60 173161 70 226204 80 201434 90 541929 100 312778 Alignments with percent identity lower than 60 deleted. # remaining Aligments : 1305042 # unique Features these represent alignments represent: 1167319 % of total features these alignments represent : 17.29 % Following is the final summary # alignments : 19246 # unique Features these alignments represent: 17249 % of total features these alignments represent : 17.25 %