Hi, this may sounds a bit trivial question, i indexed my ref genome, along with the indexed genome, there is also a file called .fasta.fai. My question is what is in the fasta.fai? I opened this file, it does not have any header. Did I do anything wrong ?
I then used the ref genome to call SNPs. I assume some sort of position information is used to tell me the position of snps in the ref genome. Which column is position? Thanks.
Here is a subset of the fasta.fai file
gi|394055774|gb|AGTA02000001.1| 5516 93 70 71 gi|394055773|gb|AGTA02000002.1| 2292 5781 70 71 gi|394055772|gb|AGTA02000003.1| 4668 8199 70 71 gi|394055771|gb|AGTA02000004.1| 1190 13027 70 71