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
<p>The fasta.fai <em>is</em> the fasta <strong>index</strong>, and the one you posted looks legit.</p>

<p>For each row:</p>

<p>Column 1: The contig name. In your FASTA file, this is preceeded by &#39;&gt;&#39;</p>

<p>Column 2: The number of bases in the contig</p>

<p>Column 3: The byte index of the file where the contig sequence begins. (Notice how it constantly increases by roughly the amount in column 2?)</p>

<p>Column 4: <strong>bases </strong>per line in the FASTA file</p>

<p>Column 5: <strong>bytes </strong>per line in the FASTA file</p>
