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Table 2 Mapping statistics for sea bass BAC-ES comparatively mapped to the stickleback chromosomes I to VII.

From: The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

A stickleback chromosome ALL CHR CHR I CHR II CHR III CHR IV CHR V CHR VI CHR VII
  stickleback chromosome size [bp] 400,788,495 28,185,914 23,295,652 16,798,506 32,632,948 12,251,397 17,083,675 27,937,443
  genetic linkage group sea bass - LG13 LG5 LG10 LG2/? LG1 LG11 LG3/LG14
B sea bass BAC-contigs 588 (816) 34 (58) 28 (44) 24 (29) 42 (62) 16 (28) 24 (36) 43 (65)
  largest BAC-contig [bp] 8,860,934 (5,034,967) 6,029,661 (4,511,889) 4,235,816 (2,100,554) 3,575,021 (2,455,450) 7,720,774 (3,886,881) 1,931,357 (1,573,884) 8,860,934 (5,034,967) 4,327,197 (2,521,767)
  % of chr. covered by BAC-contigs 87.0% (78.1%) 84.8% (75.6%) 90.0% (83.6%) 85.5% (76.0%) 86.6% (76.2%) 88.5% (83.4%) 85.3% (77.5%) 89.3% (78.9%)
  number of BACs in min. tiling path 3,929 (3,629) 271 (257) 227 (221) 161 (144) 313 (283) 121 (118) 162 (147) 281 (266)
  paired end aligned consistent BACs 20,635 (12,076) 1,465 (802) 1,254 (772) 874 (510) 1,593 (883) 731 (418) 993 (678) 1,486 (849)
  one end aligned BACs 24,940 (25,845) 1,759 (1,781) 1,399 (1,453) 1,199 (1,196) 2,012 (2,111) 784 (839) 1,052 (1,087) 1,855 (1,940)
C inconsistently aligned same chr. 1,487 (1,920) 98 (128) 77 (100) 93 (128) 111 (152) 57 (80) 64 (96) 97 (132)
  potential intra-chr. rearrangements between stickleback and sea bass 214 12 8 17 10 6 9 14
  intra-chr. rearrangements also found between medaka and stickleback 139 9 5 17 8 2 1 10
  BAC-contigs with same neighbour in medaka as in stickleback 149 7 4 4 16 4 7 7
D total annotated genes in ensembl 19,045 1,253 853 923 1,317 733 749 1,311
  % genes covered by BAC-contigs 85.4% (77.5%) 80.5% (73.9%) 85.2% (78.8%) 86.5% (79.2%) 88.3% (79.3%) 88.4% (83.2%) 78.2% (72.0%) 86.7% (76.1%)
  1. Rows (A) show a summary of the 21 reference chromosomes (stickleback assembly: BROAD S1, Feb 2006) and the known corresponding genetic linkage groups of sea bass according to Chistiakov et al. [30]. Rows (B) summarize consistently mapped BAC-ES, BAC-contigs and reference genome/chromosome coverage of the minimal tiling path. Rows (C) focus on inconsistently mapped BAC-ES, which where further analysed for potential intra-chromosomal rearrangements and compared to the medaka genome as a second reference genome. Rows (D) display the number of annotated genes in stickleback and the percentage of them covered by the sea bass BAC-map. Values in brackets "()" show results for a comparative map that was built by using only BAC-ES data, while all other values represent results of improved mapping using BAC-ES together with whole genome shotgun data.