Park et al. BMC Genomics 2012, 13:473 http://www.biomedcentral.com/1471-2164/13/473 Page 3 of 8 Figure 1 Enhanced genome annotation, single nucleotide variation analyses, and differentially expressed genes before and after exercise in horse. (A) Red and green circles indicate expressed genes in the blood and muscle tissues, respectively, and the blue circle shows the current Ensembl annotation (Release 62). The grey rectangle indicates the coverage of the current horse genome. (B) Green circle: SNPs provided by the Broad Institute, red circle: SNPs provided by Ensembl (release 62), blue circle: SNPs identified from this study. (C) SNV profiles of six horses for the titin (TTN) gene. The top of the blue arrow is the 5' end and the bottom is 3' end of TTN gene. The X-axis shows the names of the horses. Dark green horizontal bars are non-synonymous SNVs. Light green horizontal bars are synonymous SNVs. (D) Blue bars: >2-fold upregulated genes, red bars: >2-fold downregulated genes, white bars: not differentially expressed. The four pie charts display the composition of the DEGs supported by four horses (white), five horses (light grey), and six horses (grey). SOAPdenovo [28], resulting in assemblies of 42,476 to 72,011 scaffolds for each sample. These assembled sequences increased the extent of the current horse genome (Additional file 1: Supplementary Methods, Additional file 1: Figure S2, and Additional file 1: Tables S5, S6, S7, S8). When we pooled the scaffolds together, we identified around 670,000 non-redundant unigenes. 27% to 46% of these unigenes from each sample were matched to human genes using tBLASTx (Additional file 1: Table S9). Identification and dissection of novel SNVs from a large amount of horse RNA-Seq sequences We identified 182,722 non-redundant SNPs and 7,251 non-redundant INDELs from the 24 samples using several filters, including an exon-intron boundary misalignment