TABLE 1.

Details for DNA-Seq consistency for Scaff2links assemblies in comparison to reference-assisted scaffolding.

Features*	Scaffolds «Phylo»	Difference with
		«union100»	«union10»
Number of mapped#	764,982,145	+20	−126
Number of properly paired	758,804,408	+358	+26
Number of Singletons	2,288,435	−26	+94
Number with mate mapped to a different fragment	309,158	−132	+276
Number with mate mapped to a different fragment (mapQ ≥ 5)	219,998	+16	+48

*More detailed view of DNA-Seq consistency within scaffold assemblies after secondary scaffolding. The table focus on differences between union100 and union10 assemblies which differ in the minimum number of reads to support a linkage through mRNA-Seq. DNA-Seq consistency is expressed in terms of short-read alignment statistics. ^#“Mapped” stands for the number of reads mapped. “Properly paired” stands for the number of reads that are properly paired (right strand and insert size range). A Singleton is a read with an unmapped mate. mapQ corresponds to a pared quality score of a read alignment.