BMC Genomics 2009, 10:295 http://www.biomedcentral.com/1471-2164/10/295 Table 1: Summary of LongSAGE tags sequenced from B. napus seeds at 23 and 35 days after pollination (DAP). 23 DAP library 35 DAP library Combined data Category Unique sequences All sequences Unique sequences All sequences Unique sequences All sequences Total extracted ditags Rejected ditags (Phred score ≤ 20a) Accepted ditags (Phred score > 20a) Total extracted tags Accepted tags (excluding polyA tags) Copy number of accepted tags - - 23,996 24,655 24,654 34,984 10,685 24,299 48,534 48,514 - - 11,846 12,714 12,713 15,919 3,306 12,613 25,198 25,183 - - 35,842 37,369 37,367 50,903 13,991 36,912 73,732 73,697 1 2–5 6–20 21–99 >100 18,183 (73.8.%) 5,329 (21.6%) 1,016 (4.1%) 118 (0.5%) 8 (0.03%) 18,183 (37.5%) 14,320 (29.5%) 9,450 (19.5%) 4,437 (9.1%) 2,124 (4.4%) 9,741 (76.6%) 2,510 (19.7%) 406 (3.2%) 46 (0.4%) 9 (0.07%) 9,741 (38.7%) 6,596 (26.2%) 3,668 (14.6%) 1,997 (7.9%) 3,181 (12.6%) a Using Sage-phred.pl, including duplicated ditags amounted to about 80% (Table 2). This discrepancy might be due to the reduced numbers of ESTs in the data- base derived from transcripts expressed at low levels, com- pared to transcripts expressed at high levels within B. napus seeds. Broadly different estimates exist on the pro- portion of errors within tag sequences caused by experi- mental artefacts, ranging from 1.67% to 15.6% of LongSAGE tags [13,14] with at least one erroneous base- pair introduced by sequencing. However, the singleton tag category might contain a higher proportion of tags with sequencing artefacts, also contributing to the different ratio of successfully matched tags in the singleton and ≥ 2 count categories. 12,728 tags from library 23 DAP were matched to 7,208 of 20,462 Brassica EST-matched A. thal- iana proteins. 7,232 tags from library 35 DAP were matched to 4,875 A. thaliana proteins (Table 2). Table 2: Summary of LongSAGE tag-to-gene mapping data for two libraries from B. napus seeds at 23 and 35 days after pollination (DAP). Analysis including all singleton tags 23 DAP library 35 DAP library combined data Number of Brassica ESTs matched to the A. thaliana proteome Number of A. thaliana genes matched by Brassica ESTs Number of tags accepted for processing Number of Brassica ESTs matched by tags Total number of accepted tags matched to Brassica ESTs Number of accepted tags not matched to any Brassica EST Number of accepted singleton tags matched to Brassica ESTs Number of accepted tags with ≥2 counts matched to Brassica ESTs Number of A. thaliana genes matched via Brassica ESTs and tags Number of A. thaliana genes matched and oriented via Brassica ESTs and tags (putative chimeric ESTs removed) Number of genes matched in both directions Number of genes matched in sense orientation exclusively Number of genes matched in antisense orientation exclusively 24,654 12,713 32,395 256,420 214,981 301,180 12,728 of 24,654 (51.6%) 7,232 of 12,713 (56.9%) 15,955 of 32,395 (49.3%) 11,926 of 24,654 (48.4%) 5,481 of 12,713 (43.1%) 16,400 of 32,395 (50.6%) 7,615 of 18,183 (41.9%) 5,513 of 6,471 (85.2%) 4,819 of 9,741 (49.5%) 2,413 of 2,972 (81.2%) 11,421 of 26,498 (43.1%) 6,010 of 7,727 (77.8%) 7,208 4,478 1,125 (25.1%) 3,057 (68.3%) 296 (6.6%) 834,732 20,462 4,875 3,005 560 (18.6%) 2,242 (74.6%) 203 (6.8%) 8,255 5,120 1,453 (28.4%) 3,358 (69.5%) 309 (6.1%) Page 3 of 16 (page number not for citation purposes)