Hello everyone, I have aligned a bunch of whole genome shotgun sequencing data against Pangenome protein sequences by using DIAMOND protein aligner to find out which genes are present and which are absent in my DNA sequence data . I am sorry if my question is dumb, but I am new in alignment and learning. I have some genes which are 100% matched with mutiple DNA sequences, please see the example below! (this the output of DIAMOND which is Blast tabular file format)
HWI-ST913:300:C5W5DACXX:7:1207:13092:33669 Ha15_00039042 100.0 24 0 0 3 74 183 206 1.5e-07 51.6 HWI-ST913:300:C5W5DACXX:7:1208:1383:39276 Ha15_00039042 100.0 26 0 0 22 99 175 200 1.3e-09 58.5 HWI-ST913:300:C5W5DACXX:7:1208:3015:81325 Ha15_00039042 100.0 29 0 0 2 88 178 206 1.1e-10 62.0
I want to know what does this mean? Is this something that I should expect or something is going wrong? Thanks for any help or providing me with some references to learn about this!