I am running GWAS analyses with gemma that seem to work but when I open the centered relatedness matrix (.cXX), I do get a symmetric matrix but the main diagonal is not made of 1s ... why?

The [manual][1] p.11 part 3.3.1 shows an example of matrix with a main diagonal which is not made of 1s. 
I also tried to dig into the [gemma code][2] on Github but I did not find the piece of code used to calculate the relatedness matrix.

---
####Commands and output

Plink and gemma commands to generate the matrix:

    # Generate plink file from my VCF file (67 samples)
    vcftools --gzvcf $vcf_file --plink --out $prefix_vcf
    # Make binary plink files
    plink --file $prefix_vcf --make-bed --out $prefix_vcf
    # Generate centered relatedness matrix with gemma
    gemma -bfile $prefix_vcf -gk 1 -o $prefix_vcf

Here the output log of gemma:

    ##
    ## GEMMA Version = 0.94
    ##
    ## Command Line Input = -bfile subset_67_accessions_wo_singletons_only_alt_allele -gk 1 -o subset_67_accessions_wo_singletons_only_alt_allele
    ##
    ## Summary Statistics:
    ## number of total individuals = 67
    ## number of analyzed individuals = 67
    ## number of covariates = 1
    ## number of phenotypes = 1
    ## number of total SNPs = 927314
    ## number of analyzed SNPs = 39678
    ##
    ## Computation Time:
    ## total computation time = 0.123833 min
    ## computation time break down:
    ##      time on calculating relatedness matrix = 0.00733333 min
    ##

I get as expected a square matrix of order 67 (as my number of samples in the VCF file).
Here are the first 5 rows and columns of the matrix:

    0.5265889259    0.0918289748    0.01315201643    -0.02417258371    -0.00300349980
    0.0918289748    0.4426259465    0.01751500729    -0.0196104412    -0.04093555612
    0.01315201643    0.01751500729    0.494663962    0.01773204554    0.03579284737
    -0.02417258371    -0.0196104412    0.01773204554    0.5622735808    0.05660374681
    -0.003003499807    -0.04093555612    0.03579284737    0.05660374681    0.6064086438    

There is symmetry but not a main diagonal of 1s while same individuals should be identical to themselves, shouldn't they?

*NB*: I posted a similar post on the [gemma-discussion][3] google group but still did not get an answer after a month.


  [1]: http://www.xzlab.org/software/GEMMAmanual.pdf
  [2]: https://github.com/genetics-statistics/GEMMA/tree/master/src
  [3]: https://groups.google.com/forum/#!topic/gemma-discussion/34FyII8oXUM
I've got the answer from the creator of GEMMA Xiang Zhou: 

> The centered relatedness matrix does not scale each column of the genotype matrix, so the main diagonal of the resulting relatedness matrix will not be close to 1s (usually around 0.3 depending on maf etc.). If you use the scaled relatedness matrix (.sXX), then the main diagonal should be made of values that are very close to 1s.

