i have used NOVOPlasty to assemble Santalum album chloroplast reads from whole-genome sequencing data and got two possible assemblies. After BLASTn with reference Santalum album chloroplast genome(subject) I![enter image description here] got the DOT PLOT graph but unable to understand how it is telling the orientation of the SSC region and which assembly to choose for annotation.
Don't know how to attach the screenshot of the dot plot with this question. Please help me.