From: Finding the missing honey bee genes: lessons learned from a genome upgrade
 | All OGSv3.2 | Type I new genes | Type II new genes | Previously known genes | |
---|---|---|---|---|---|
 | Number of genes (% of total OGSv3.2 genes) | 15,314 (100%) | 782 (5.1%) | 3,953 (25.8%) | 10,579 (69.1%) |
Scaffold analysis | Number of genes within mapped scaffolds (% of no. of gene type) | 13,285 (86.8%) | 544 (69.6%) | 3,199 (80.9%) | 9,542 (90.2%) |
Number of genes within un-mapped scaffolds (% of no. of gene type) | 2,029 (13.2%) | 238 (30.4%) | 754 (19.1%) | 1,037 (9.8%) | |
CDS analysis | Average CDS length | 1,266 | 1,172 | 330 | 1,622 |
Average no. CDS Exons | 5.3 | 5.6 | 2.1 | 6.5 | |
Number of single CDS exon genes (% of no. of gene type) | 2,059 (13.4%) | 101 (12.9%) | 1,239 (31.3%) | 719 (6.8%) | |
Number of multi-CDS exon genes (% of no. of gene type) | 13,255 (86.6%) | 681 (87.1%) | 2,714 (68.7%) | 9,860 (93.2%) | |
Intron analysis | Number of introns (% of total OGSv3.2 introns) | 66,212 (100%) | 3,585 (5.4%) | 4,333 (6.5%) | 58,294 (88%) |
Number of introns validated by EST intron coordinates (% of introns of gene type) | 54,514 (82.3%) | 2,573 (71.8%) | 1,930 (44.5%) | 50,011 (85.8%) | |
Peptide analysis | Number of genes with a peptide match (% of no. of gene type) | 3,631 (23.7%) | 132 (16.9%) | 82 (2.1%) | 3,417 (32.3%) |
Protein analysis | No. of genes with overlap to at least one protein alignment (% of no. of gene type) | 6,778 (44.3%) | 270 (34.5%) | 186 (4.7%) | 6,322 (59.8%) |
No. of genes with overlap to a Dmel protein alignment (% of no. of gene type) | 1,205 (7.9%) | 38 (4.9%) | 13 (0.3%) | 1,154 (10.9%) | |
Total spliced and un-spliced expressed sequence support | No. of genes with overlap to at least one transcript alignment from any of the ten libraries (% of no. of gene type) | 13,517 (88.3%) | 704 (90.0%) | 2,771 (70.1%) | 10,042 (94.9%) |
Spliced expressed sequence analysis | No. of genes with overlap to at least one spliced transcript alignment from each of the ten libraries (% of no. of gene type) | 1,062 (6.9%) | 32 (4.1%) | 15 (0.4%) | 1,015 (9.6%) |
No. of genes with overlap to at least one spliced transcript alignment from any of the ten libraries (% of no. of gene type) | 12,172 (79.5%) | 622 (79.5%) | 2,110 (53.4%) | 9,440 (89.2%) | |
No. of genes without overlap to any spliced transcript alignments in any of the ten libraries (% of no. of gene type) | 3,142 (20.5%) | 160 (20.5%) | 1,843 (46.6%) | 1,139 (10.8%) | |
Genes broadly expressed across four tissues (% of no. of gene type) | 2,326 (15.2%) | 60 (7.7%) | 95 (2.4%) | 2,171 (20.5%) | |
Genes narrowly expressed in only a single tissue (% of no. of gene type) | 3,346 (21.8%) | 234 (29.9%) | 1,139 (28.8%) | 1,973 (18.7%) | |
No. of genes without overlap to any spliced transcript alignments in any of the four tissues (% of no. of gene type) | 3,632 (23.7%) | 192 (24.6%) | 1,985 (50.2%) | 1,455 (13.8%) | |
Analysis of alignments to other bee genomes | No. of genes that align to Aflo_1.0 (% of no. of gene type) | 13,491 (88.1%) | 566 (72.4%) | 2,584 (65.4%) | 10,341 (97.8%) |
No. of genes that align to Bter_1.0 (% of no. of gene type) | 12,262 (80.1%) | 527 (67.4%) | 1,566 (39.6%) | 10,169 (96.1%) | |
Evidence-supported genes | No. of genes with overlap to at least one form of biological evidence (% of no. of gene type) | 14,084 (92.0%) | 713 (91.2%) | 2,930 (74.1%) | 10,441 (98.7%) |
No. of genes that align to Aflo_1.0 and/or Bter_1.0 and/or overlap at least one form of biological evidence (% of no. of gene type) | 14,836 (96.9%) | 734 (93.9%) | 3,555 (89.9%) | 10,547 (99.7%) | |
GC analysis | Number of genes on GC compositional domains >10Â kb (% of OGSv3.2 total) | 15,224 (99.4%) | 777 (5.1%) | 3,923 (25.8%) | 10,524 (69.1%) |
Avg. GC content of compositional domain gene resides in | 29.60% | 26.40% | 32.00% | 28.90% | |
ENC analysis | Effective number of codons | 44.95 | 41.97 | 45.69 | 44.9 |