I tried to understand the output of bcftools mpileup, especially the I16 tag.
In this case, I16=0,9878,0,28,..., the total reads are 9878+28=9906, that not equal to the DP=9953

According to the description in header of vcf file for I16 tag, the first four numbers are:

// depth fwd   .. ref (0) and non-ref (2)    
// depth rev   .. ref (1) and non-ref (3)    

The sum of the four number supposed (I think!?) to equal to DP (raw read depth) number, but it is not.

So, I have two questions:

1. Is there any default filtering that will change the first four numbers in I16? what is it?
2. How can I tell the exact the depth for each of the ALT bases? (C, G, A in this case).

The following are the command and one line of the results:

$ bcftools mpileup -d 10000 -f ref.fa align.bam > mpileup.vcf

$ grep -P "\t311\t" mpileup.vcf
ref     311     .       T       C,G,A   0       .       DP=9953;I16=0,9878,0,28,397088,1.60422e+07,588,12502,592680,3.55608e+07,1680,100800,19953,41405,56,112;QS=0.998521,0.00121707,0.00019111,7.04091e-05;VDB=1.30483e-15;SGB=-0.693054;RPB=0.998703;MQB=1;BQB=1.00562e-18;MQ0F=0      PL      0,255,255,255,255,255,255,255,255,255

## bcftools  v1.9