Hi, I have NGS DNA sequence reads for two different plant species (A and B) in the same genera. I did sequence alignment of species A for its reference genome(G1) found for example 10000 SNPs. However, species B doesn't have a reference genome. Therefore, I selected a genome (G2), which is closely related to species B, and did the alignment and found 9500 SNPs. As cross-validation, I aligned the species A sequence reads to G2 genome. Apparently, G1 genome is twice bigger than the G2 genome. After alignment with species A reads to G2 genome, I found 30000 SPNs.
I appreciate if someone can help me to figure out the following questions.
Q1) why I get 30000 SNPs with G2 with species A? Q2) is this due to the random alignment of seq reads to a small genome? Q3) I got 30000 SNPs as the G1 and G2 are more evolutionary distance? Q4) or due to any other reasons?