The first generation of a BAC-based physical map of Brassica rapa

BMC Genomics

Table 2 Summary of the B. rapa physical map autobuild produced from assembly of the 67,468 BAC clones.

Build^a	Contigs	Avr. contig length (kb)^b	Longest contig (kb)	Genome coverage	Physical length (Mb)^b	Q clones (%)	No. of contigs of different sizes					Singletons
							≥ 100	99-50	49-25	24-10	<10
Initial 1e-45	4,726	208	7,596	1.8×	985	6,376 (9.5)	9	34	251	892	3,540	25,041
Merge 1e-40	4,057	230	5,548	1.7×	935	6,457 (9.6)	10	64	318	800	2,865	23,977
Merge 1e-30	3,001	287	7,329	1.6×	860	6,927(10.3)	24	126	384	606	1,861	21,351
Merge 1e-20	1,801	421	8,686	1.4×	759	8,832(13.1)	82	182	299	370	868	17,086
Merge 1e-15	1,417	512	9,390	1.3×	725	10,135(15.0)	111	177	241	269	619	14,001

Each HICF assembly was performed starting with a complete build, followed by iteration of the Dqer, end-merge, and singleton-merge routines by means of FPC v8.5.3.
^aAdditional Dqer, end-merge, and singleton-merge routines at 1e-35 and 1e-25 are not shown.
^bEach fingerprint band was estimated to represent an average of 1.39 kb. It was estimated by the average insert size of the BAC clones (124 kb, Table 1) divided by the total number of valid bands of 67,468 BAC clones (6,005,758 bands) used for the map contig assembly.

ISSN: 1471-2164