SNP site discovery was performed using both the DNASTAR NGEN and Newbler combined assemblies as reference transcriptomes. The Newbler gsMapper SNP calling program generated two output files. One output file contained all possible SNPs. The other output file contained only the high confidence SNP calls, which was used as the starting point for selecting SNPs for the mapping study. A summary of the SNP discovery results is displayed in Table 4. As shown in the last two columns of Table 4, 15,542 and 12,119 candidate SNP sites were discovered using the Newbler and DNASTAR reference transcriptomes, respectively. For each candidate SNP with a minimum 100 bases of sequence flanking the SNP, 50 bases from each flanking side of the SNP site was extracted for DNA marker development. The values in parenthesis in the last two rows of Table 4 represent the number of SNP sites selected, based on sufficient flanking sequence. The sequences and statistics for the high quality and most informative SNPs used in the GWAS are presented in a table in Additional file 4.Table 4Summary of SNP discovery results for F. grandifolia using the reference transcriptomes generated by DNASTAR NGEN and NewblerStatisticsDNASTAR Reference TranscriptomeNewbler Reference TranscriptomeNumber of Contigs in Reference43,21214,977Number of Bases in Reference28,676,24211,580,835Number of Mapped Reads (%)1,357,629 (96.55%)938,418 (88.82%)Number of Mapped Bases (%)494,805,288 (97.45%)312,081,222 (85.48%)Fully Mapped Reads (%)444,838 (31.64%)396,609 (37.54%)Partially Mapped Reads (%)35,728 (2.54%)135,858 (12.86%)Non-Unique Mapped Reads (%)871,685 (61.99%)147,210 (13.93%)Chimeric Reads (%)5378 (0.38%)258,741 (24.49%)Unmapped Reads (%)32,025 (2.28%)101,623 (9.62%)Reads Too Short (%)16,470 (1.17%)16,470 (1.56%)High Confidence SNP Calls2119 (12,069)15,542 (14,574)HC SNP Calls (Not Ambiguous)10,971 (10,934)15,541 (14,573)