Generation of a BAC-based physical map of the melon genome

BMC Genomics

Table 2 Summary of the C. melo physical map FPC assemblies.

Tests for initial cutoff value^a	Contigs	Singletons	Physical length (Mb)	Q clones^b
Test 1e-35	1420	1133	398	40/233
Test 1e-45	1706	1772	421	40/158
Test 1e-55	1909	2562	432	29/84
Test 1e-65	2075	3399	438	12/44
Assembly Steps ^c	Contigs	Singletons	Physical length (Mb)	Q clones ^b	Longest contig (Mb)	Number of contigs (number of contigs with > 5% Q-clones) ^d
						≥ 100	99-50	49-25	24-10	9-3	= 2
Initial 1e-45	1706	1772	1.17	421	40/158	0(0)	6(5)	63(36)	393(89)	968(28)	276(0)
DQer (1e-48 to 1e-90)	1777	1923	1.10	428	66/0	0	1	49	412	1027	288
Merge 1e-40	1750	1551	1.10	432	66/0	0	2	51	431	1017	249
Merge 1e-35	1714	1290	1.10	430	66/0	0	2	56	442	998	216
Merge 1e-30	1650	1071	1.4	426	66/0	1	3	62	449	953	182
Merge 1e-25	1577	836	1.5	421	65/0	2	3	69	462	884	157
Merge 1e-20	1491	635	2.8	415	64/0	3	5	79	456	816	132
Merge 1e-15	1355	441	3.2	407	62/0	3	9	102	428	706	107

^aAn initial test to determine the optimal cutoff value was performed with several cutoff values in the 1e-35/1e-65 range
^bNumber of contigs containing ≤/> than 5% of Q-clones
^cA cutoff value of 1e-45 was used for the initial contig assembly. Consecutive DQer (for contigs containing > 5% Q-clones), end-merge and singleton-merge steps were performed to minimize the number of singletons, contigs and Q-clones
^dDistribution according to the number of clones belonging to each contig

ISSN: 1471-2164