A first generation BAC-based physical map of the channel catfish genome

BMC Genomics

Table 3 Verification of physical map integrity by linkage mapping of clones from each end of the contig

Contig	Number of Clones	Length (kb)	Left clone	Right clone	Most distal internal clone	r¹	LOD²	Linkage Group
Contigs with markers on terminal BAC clones
13	93	848	GY144N04	GY135E18	not used	0.09	7.91	U14
23	138	1136	GY121F03	GY034A19	not used	0.02	11.45	Unknown³
43	121	807	GY105H22	GY113C07	not used	0.01	29.49	U05
58	106	753	GY107P06	GY106D19	not used	0.01	25.59	U23
104	99	767	GY110K13	GY031O20	not used	0.01	49.69	U22
150	128	1233	GY116H16	GY082C02	not used	0.03	19.63	U09
158	96	816	GY085J18	GY119G01	not used	0.01	51.17	U05
220	130	1429	GY061E20	GY127H06	not used	0.09	15.29	U28
321	91	599	GY082H04	GY115E15	not used	0.04	20.51	Unknown³
358	96	1068	GY063K13	GY132P10	not used	0.01	24.10	U17
375	103	1006	GY014A20	GY113J02	not used	0.06	18.00	U10
422	92	816	GY143D16	GY069G22	not used	0.02	31.16	U04
1994	120	1070	GY124F07	GY125G21	not used	0.02	10.58	U27
Contigs with markers on one terminal BAC clone
191	89	694	GY016M05	n/a	GY014G05*	0.05	9.41	U26
224	129	1180	n/a	GY001C07	GY098F03*	0.00	13.55	U16
249	156	1064	GY105F13	n/a	GY074J11*	0.01	38.07	U22
2069	128	1034	n/a	GY006O05	GY138C24*	0.00	13.55	U13
2122	106	409	n/a	GY016J21	GY097F03*	0.00	13.85	U14
Mis-joined contig
84a	139	1402	GY137K09	n/a	GY048N07*	0.00	40.34	U22
84b	139	1402	n/a	GY137B18	GY020C24*	0.00	13.25	U16

¹ Percent recombination based on two-point linkage
² Log₁₀ likelihood ratio of linkage vs. non-linkage
³ No linkage to markers on the current genetic map
* When a polymorphic marker was not available (n/a) for a terminal BAC clone, this most distal mapped clone was used for linkage analysis.

ISSN: 1471-2164