A first generation BAC-based physical map of the rainbow trout genome

BMC Genomics

Table 4 Validation of physical map assembly by linkage mapping of microsatellites isolated from clones that were part of 11 of the largest contigs in the rainbow trout physical map.

Contig	No. of Clones (Q)^a	Contig Length (Kb)	No. of Markers	r^b	LOD	Chr.
58	174 (3)	1,938	2	0.000	29.2	1
84^c	190 (3)	2,300	2	0.014	19.1	18
100	313 (2)	3,300	2	0.101	20.6	27
168	306 (3)	2,934	2	0.009	28.7	10
172	299 (6)	3,167	3	0.040	8.1	6
260^c	224 (1)	2,692	4	0.039	31.3	2
336	136 (0)	1,722	3	0.005	46.3	3
791^c	124 (0)	1,722	2	0.000	25.2	22
930	112 (1)	1,394	2	0.006	49.7	11
Mis-joined Contigs
138a	431 (4)	4,590	2	0.043	16.0	1
138b	431 (4)	4,590	1	N/A	32.0	27
450a	334 (4)	3,709	2	0.006	38.6	22
450b	334 (4)	3,709	1	N/A	39.4	1

^aNumber of Q-clones in parenthesis. Clones that were assigned to a contig but may be false positives (e.g. chimerical clones) are marked by FPC as Q-clones.
^bTwo point linkage recombination between markers from the two most distant clones in the contig.
^cAdditional markers that were previously isolated from other BACs in the contigs were linked to the new BAC end sequence microsatellites by two point linkage analysis and included in this table. Contig 84: OMM3090/MHCI-A [27]; Contig260: OMM3079/TAP1 [23]; Contig 791: OMM3183/TLR8a (manuscript in preparation).

ISSN: 1471-2164