Transcriptome sequencing for SNP discovery across Cucumis melo

BMC Genomics

Table 3 Number of SNPs shared and differential between groups

	Piel de Sapo	Inodorus	Melo	Cantalupensis	Momordica	Conomon	Agrestis acidulus	African agrestis
	Pool8	Pool7	Pool6	Pool5	Pool4	Pool3	Pool2	Pool1
Piel de Sapo		15,560	9,149	19,451	21,566	14,168	14,488	18,172
Pool8		(36/20)	(21/22)	(45/19)	(50/16)	(33/17)	(33/15)	(42/16)
*inodorus*	1,564		16,255	33,966	40,668	25,165	26,914	32,236
Pool7			(20/40)	(43/33)	(51/31)	(32/31)	(34/28)	(41/26)
*melo*	3, 260	2,722		19,727	23488	13,541	15,589	17,157
Pool6				(19/48)	(58/18)	(33/17)	(38/16)	(42/15)
*cantalupensis*	4,735	4,353	3, 178		52,514	31,461	34,510	39,016
Pool5					(51/40)	(31/39)	(34/36)	(38/33)
*momordica*	4,441	4, 484	2, 417	4,224		38,384	47,491	46,865
Pool4						(47/29)	(49/36)	(40/35)
*conomon*	19,942	20,281	12,628	14,978	9,576		27,670	33,783
Pool3							(29/34)	(35/29)
*agrestis-acidulus*	11,402	12,009	6,837	9,577	5,273	6,474		36,162
Pool2								(44/31)
African *agrestis*	20,501	20,931	14,132	18,294	13, 070	21,490	11,180
Pool1

Numbers in the upper half of the table indicate the number of common SNPs between each pair of libraries. Numbers in brackets indicate percentages these common SNPs represent of the total SNP set detected within the corresponding library (row/column). For example, there are 15,560 SNPs common between pools 8 and 7 (that is with two alleles or more in each of these pools). This number represents the 36% and 20% of the total SNPs detected within Pool 8 and pool 7 (indicated in Table2) respectively.
Numbers in the lower part of the table indicate the SNPs that are fixed within each pair of libraries, but polymorphic between them. For example, there are 1,564 SNPs for which all reads from pool 8 have one allele and all reads from pool 7 have the alternative allele.

ISSN: 1471-2164