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 Agrestis3 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).

Blanca et al.

Blanca et al. BMC Genomics 2012 13:280   doi:10.1186/1471-2164-13-280

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