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Table 2 Effects of the SNP detected in coding sequences in the collection of 92 red fruited accessions

From: Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection

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
  1. Effects are detected with SnpEff with tomato annotation ITAG 2.3 version.