The SNP detection report of the Cocoa EST

The program, Auto SNP were used to find the SNP among the available Cocoa EST.

Results Bean and Leaf Defense related Red Leaves Total Total sequences analysed 3254 1248 2 4504 No of contigs and singletons made 424, 0 359, 0 1, 0 784 Total SNPs detected 2204 1005 30 3239 Total consensus size 215576 bp 152008 bp 310bp 367894bp SNP frequency 1.02/100 bp 0.66/100 bp 9.68/100 bp 3.78/100bp Smallest contig 2 sequences 2 sequences 0 Sequences 4 Sequences Transitions C / T = 293 G / A = 263 Total =556 C / T = 194 G / A = 188 Total =382 C / T = 11 G / A = 1 Total =12 C / T = 498 G / A = 452 Total =950 Transversions A / T = 206 C / G = 118 G / T = 272 A / C = 109 Total = 105 A / T = 61 C / G = 71 G / T = 286 A / C = 135 Total = 553 A / T = 6 C / G = 0 G / T = 4 A / C = 0 Total = 10 A / T= 273 C / G= 189 G / T= 562 A / C= 244 Total =1268 Indels A = 233 C = 181 G = 264 T = 265 Total =943 A = 10 C = 12 G = 21 T = 27 Total = 70 A = 4 C = 3 G = 1 T = 0 Total = 8 A = 247 C = 196 G = 286 T = 292 Total =1021