Hi

I use Spades to generate scaffolds and then to compare to a database with reference sequences (size of the gene 399 bp). Afterwards I chose the best reference sequences mapping any scaffolds (based on the bitscore value, alignment length...) and I use them to do mapping with my FASTQ files.

I have selected two reference sequences to use according to the best results I had after blasting the database and my scaffolds (these are some of the data that I had)

NODE_19_length_207_cov_30690_ID_37, Bitscore= 316, alignment length= 203, 94.58%... mapping to reference 3a
NODE_4_length_229_cov_2.02299_ID_7, Bitscore= 283, alignment length= 183, 83.61%... mapping to reference 1a

Even if both scaffolds have quite similar values, after mapping using both reference sequences, it looks like the one selected using the NODE_4 doesn't map to my reads.

Does anyone knows the reason why? Could it be because the coverage is different?

Thanks