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Table 3 Mapping statistics for sea bass BAC-ES comparatively mapped to the stickleback chromosomes VIII to XIV.

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

A stickleback chromosome CHR VIII CHR IX CHR X CHR XI CHR XII CHR XIII CHR XIV
  stickleback chromosome size [bp] 19,368,704 20,249,479 15,657,440 16,706,052 18,401,067 20,083,130 15,246,461
  genetic linkage group sea bass LG4 LG7 LG9 LG8 ? LG20 LG19
B sea bass BAC-contigs 30 (44) 37 (45) 31 (37) 30 (27) 27 (35) 26 (38) 18 (33)
  largest BAC-contig [bp] 4,711,769 (3,129,353) 3,058,355 (1,487,429) 1,368,409 (1,368,348) 4,014,839 (3,993,770) 4,710,925 (2,950,196) 3,478,171 (3,182,188) 3,545,956 (1,757,446)
  % of chr. covered by BAC-contigs 85.8% (77.0%) 82.9% (69.7%) 84.2% (75.4%) 83.3% (74.4%) 88.5% (78.1%) 90.6% (81.8%) 88.0% (77.5%)
  number of BACs in min. tiling path 188 (177) 195 (174) 152 (140) 155 (147) 177 (160) 194 (176) 150 (142)
  paired end aligned consistent BACs 869 (517) 855 (448) 712 (410) 816 (494) 902 (559) 1,121 (678) 792 (414)
  one end aligned BACs 1,002 (1,190) 1,190 (1,168) 897 (879) 1,101 (1,089) 1,211 (1,364) 1,194 (1,266) 931 (1,017)
C inconsistently aligned same chr. 110 (112) 84 (90) 90 (118) 81 (86) 58 (90) 42 (80) 59 (62)
  potential intra-chr. rearrangements between stickleback and sea bass 10 12 16 13 12 9 6
  intra-chr. rearrangements also found between medaka and stickleback 5 9 13 7 9 3 2
  BAC-contigs with same neighbour in medaka as in stickleback 15 12 6 8 6 7 9
D total annotated genes in ensembl 876 1,009 802 1,050 1,000 970 738
  % genes covered by BAC-contigs 83.4% (75.9%) 80.0% (70.5%) 81.2% (70.7%) 83.5% (75.3%) 86.8% (76.5%) 89.6% (81.6%) 85.2% (74.9%)
  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.