Table 2 Effects of the SNP detected in coding sequences in the collection of 92 red fruited accessions
Gene name | Gene ID | exon number | CDS lenght | exon length sequenced | SNP in coding sequences | Non synonymous SNPs | Synonymous SNPs | SNP in 3' UTR | SNP in 5' UTR | SNP in splicing site | SNP in STOP codon |
|---|---|---|---|---|---|---|---|---|---|---|---|
AG | Solyc02g071730.2.1 | 5 | 5074 | 426 | 3 | 0 | 3 | 0 | 0 | 0 | 0 |
ANT | Solyc04g077490.2.1 | 7 | 3097 | 1893 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
AGO1 | Solyc03g098280.2.1 | 19 | 6274 | 2650 | 25 | 6 | 19 | 3 | 0 | 0 | 0 |
BAM1 | Solyc02g091840.2.1 | 2 | 3625 | 3514 | 32 | 6 | 26 | 4 | 7 | 0 | 0 |
CLV1 | Solyc04g081590.2.1 | 2 | 3926 | 2436 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
CLV2 | Solyc04g056640.1.1 | 1 | 2240 | 2240 | 4 | 3 | 1 | 0 | 0 | 0 | 0 |
CNA | Solyc03g120910.2.1 | 14 | 6463 | 2109 | 15 | 4 | 11 | 2 | 0 | 0 | 0 |
FIL | Solyc01g091010.2.1 | 7 | 3194 | 1070 | 7 | 3 | 4 | 3 | 3 | 0 | 0 |
FW2.2 | Solyc02g090730.2.1 | 3 | 669 | 610 | 5 | 1 | 4 | 2 | 0 | 0 | 0 |
KAPP | Solyc01g079720.2.1 | 8 | 14613 | 1118 | 9 | 4 | 5 | 2 | 0 | 0 | 0 |
KOR1 | Solyc01g102580.2.1 | 6 | 3289 | 2509 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
LAS | Solyc07g066250.1.1 | 1 | 1286 | 1286 | 29 | 6 | 23 | 0 | 0 | 0 | 0 |
LC | Solyc02g083940.2.1 | 1 | 5663 | 164 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
OVATE | Solyc02g085500.2.1 | 2 | 1383 | 1186 | 2 | 2 | 0 | 3 | 0 | 0 | 1 (lost) |
PHB | Solyc02g024070.2.1 | 15 | 5882 | 2362 | 9 | 4 | 5 | 0 | 2 | 0 | 0 |
PHV | Solyc08g066500.2.1 | 15 | 5274 | 2225 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
RBL | Solyc02g081680.2.1 | 14 | 4985 | 2650 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
REV | Solyc11g069470.1.1 | 18 | 5512 | 2508 | 43 | 5 | 38 | 0 | 0 | 1 | 0 |
SP/TFL1 | Solyc06g074350.2.1 | 2 | 1929 | 510 | 5 | 2 | 3 | 2 | 0 | 0 | 0 |
SHD | Solyc04g081570.2.1 | 15 | 5102 | 2769 | 28 | 6 | 22 | 4 | 3 | 0 | 0 |
STM | Solyc02g081120.2.1 | 4 | 3426 | 1592 | 6 | 3 | 3 | 4 | 1 | 0 | 0 |
SYD | Solyc02g068560.2.1 | 4 | 14883 | 3334 | 44 | 22 | 22 | 1 | 0 | 0 | 0 |
SUN | Solyc10g079240.1.1 | 5 | 2229 | 1261 | 15 | 10 | 5 | 0 | 0 | 0 | 1 (gained) |
TD380 | Solyc02g085390.2.1 | 5 | 7707 | 577 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
TPL | Solyc03g117360.2.1 | 25 | 9952 | 3043 | 29 | 4 | 25 | 9 | 0 | 0 | 0 |
ULT1 | Solyc07g054450.2.1 | 3 | 3273 | 699 | 4 | 1 | 3 | 3 | 2 | 0 | 0 |
UFO | Solyc02g081670.1.1 | 2 | 1367 | 1367 | 20 | 7 | 13 | 0 | 0 | 0 | 0 |
WUS | Solyc02g083950.2.1 | 3 | 1238 | 1003 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
ZLL | Solyc09g082830.2.1 | 18 | 6153 | 2652 | 37 | 8 | 29 | 0 | 0 | 1 | 0 |
Supplementary genes within resequenced fragments | |||||||||||
Adenylosuccinate synthetase | Solyc02g085520.2.1 | 1 | 8807 | 231 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
AHRD V1 - MDTK | Solyc02g090740.2.1 | 1 | 1608 | 1582 | 13 | 8 | 5 | 5 | 0 | 0 | 0 |
AHRD V1 - Q9LIL2_ARATH | Solyc01g102570.2.1 | 1 | 1314 | 62 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
ATP dependent RNA helicase | Solyc04g081580.2.1 | 2 | 6006 | 655 | 4 | 1 | 3 | 15 | 0 | 0 | 0 |
Glucosyltransferase | Solyc02g081690.1.1 | 1 | 1445 | 1445 | 11 | 4 | 7 | 0 | 0 | 0 | 0 |
Os01g0786800 protein | Solyc02g085400.2.1 | 3 | 2736 | 496 | 3 | 0 | 3 | 3 | 0 | 0 | 0 |
Ovate protein | Solyc02g085510.1.1 | 1 | 179 | 179 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |