Transcriptome sequencing for SNP discovery across Cucumis melo

BMC Genomics

Table 4 Polymorphism in Cm-ACO-1 and Cm-eiF4-iso detected by SOLiD sequencing and EcoTILLING[59]

Position in the scaffold¹	Position in the gene (from ATG)	SNP MAF	aa change	Effect on protein according to SIFT²	Exon	Detected by SOLiD/EcoTILLING	Agrestis ³	Momord	Melo
Coding region of Cm-ACO-1, CM3.5_scaffold00022
3015744	41	A/G	D14G	Tolerated (1.00/3.02)	1	Yes/yes	G:6,7,4	A:21	A:5,2,8,-
		0.68
3015944	241	A/G	L46L		2	Yes/yes	G:15,6,5	A:15	A:5,5,8,1
		0.54						G:1	G:1,0,1,0
3016016	313	T/G	L70L		2	Yes/yes	G:0,3,2	T:12	T:8,2,11,6
		0.99
3016091	388	T/A	L95L		2	Yes/yes	T:3,1,0	T:10	T:7,-,2,2
		0.80					A:0,0,6
3016304	601	C/A	L131M	Not tolerated	3	Yes/yes	C:8,4,6	C:12	C:9,4,20,5
		0.87		(0.03/3.02)				A:10
-	747	C/T	D179D		3	No/yes
3016920	1216	T/C	V294A	Tolerated	4	Yes/no	T:11,7,7	T:29	T:18,5,20,7
		0.97		(0.12/3.03)				C:1	C:1,0,0,1
Coding region of Cm-eiF(iso)4E, CM3.5_scaffold00057
-	26	G/A	G9D	Not tolerated	1	No/yes
				(0.00/4.32)*
1030561	41	C/T	A14V	Not tolerated	1	Yes/yes	G:2,3,3	G:3	G:5,1,5,1
		0.90		(0.00/4.32)*			A:4,0,0
1030440	162	T/C	L54L		1	Yes/yes	G:31,22,3	G:12	G:31,1,5,0
		0.70					T:0,1,0	T:1	T:3,3,21,7
1029938	664	C/T	S112N	Tolerated	2	Yes/no	C:66,33,26	C:25	C:0,15,55,19
		0.99		(0.56/3.11)			T:2,0,0		T:4,0,1,0
1029710	892	A/G	L153L		3	Yes/no	A:91,49,30	A:46	A:75,17,54,30
		0.99					G:1,0,0		G:1,1,0,0
1029697	905	C/T	K158E	Not tolerated	3	Yes/no	T:0,38,13	T:31	T:67,10,39,26
		0.99		(0.02/3.12)			C:5,0,0		C:3,0,0,0
1028781	1810	C/T	D178G	Tolerated	4	Yes/no	T:0,23,17	T:17	T:57,17,27,26
		0.99		(0.65/3.12)			C:7,0,0		C:1,0,2,0
1028629	1962	C/T	K198K		5	Yes/no	T:33,24,26	T:34	T:34,4,35,17
		0.99							C:2,0,1,0
1028619	1972	C/T	S202G	Not tolerated	5	Yes/no	T:42,32,33	T:37	T:52,8,49,21
		0.99		(0.00/3.14)				C:2	C:1,0,0,0

¹ Position in the melon genome assembly v3.5 available at MELONOMICS[36].
² The effect of mutations was analyzed with SIFT[64]. Prediction score and median sequence conservation, respectively, are indicated in brackets. * Low confidence in the prediction (few sequences represented at those positions).
³ Number of reads of each allele are indicated in each pool, (−) means that this nucleotide has not been sequenced in the corresponding pool, numbers are ordered according to pool number, agrestis (pools 1, 2 and 3), momord (pool 4), melo (pools 5, 6, 7, 8).

ISSN: 1471-2164