Why does the AD value of my VCF file display 3 values?

Question

[mgranada3]

I have been trying to calculate the allele frequency in my data per these instructions given to me.

However, I got to a sample which has 3 values for the AD column.

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  FR06_AU1_150_S12
ChrA_C_glabrata_CBS138  185059  .   T   G   400.64  QD_filter   AC=1;AF=0.500;AN=2;BaseQRankSum=-5.514;DP=323;ExcessHet=0.0000;FS=51.624;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=1.71;ReadPosRankSum=-2.736;SOR=0.040;ANN=G|5_prime_UTR_variant|MODIFIER|CAGL0A01738g|CAGL0A01738g|transcript|CAGL0A01738g-T|protein_coding|1/1|c.-529T>G|||||529|,G|upstream_gene_variant|MODIFIER|CAGL0A01672g|CAGL0A01672g|transcript|CAGL0A01672g-T|protein_coding||c.-3491A>C|||||3464|,G|upstream_gene_variant|MODIFIER|CAGL0A01694g|CAGL0A01694g|transcript|CAGL0A01694g-T|protein_coding||c.-1244A>C|||||1194|,G|downstream_gene_variant|MODIFIER|CAGL0A01716g|CAGL0A01716g|transcript|CAGL0A01716g-T|protein_coding||c.*209T>G|||||89|,G|downstream_gene_variant|MODIFIER|CAGL0A01760g|CAGL0A01760g|transcript|CAGL0A01760g-T|protein_coding||c.*2197A>C|||||2145|,G|downstream_gene_variant|MODIFIER|CAGL0A01782g|CAGL0A01782g|transcript|CAGL0A01782g-T|protein_coding||c.*4607A>C|||||4338| GT:AD:DP:GQ:PL  0/1:170,64:234:99:408,0,4106
ChrA_C_glabrata_CBS138  357752  .   T   G   232.64  FS_filter;QD_filter;ReadPosRankSum_filter;SOR_filter    AC=1;AF=0.500;AN=2;BaseQRankSum=-14.586;DP=1779;ExcessHet=0.0000;FS=135.229;MLEAC=1;MLEAF=0.500;MQ=59.98;MQRankSum=-2.448;QD=0.15;ReadPosRankSum=-11.495;SOR=10.961;ANN=G|upstream_gene_variant|MODIFIER|CAGL0A03300g|CAGL0A03300g|transcript|CAGL0A03300g-T|protein_coding||c.-5428A>C|||||4544|,G|downstream_gene_variant|MODIFIER|CAGL0A03322g|CAGL0A03322g|transcript|CAGL0A03322g-T|protein_coding||c.*3236T>G|||||2944|,G|downstream_gene_variant|MODIFIER|CAGL0A03344g|CAGL0A03344g|transcript|CAGL0A03344g-T|protein_coding||c.*726T>G|||||324|,G|downstream_gene_variant|MODIFIER|CAGL0A03366g|CAGL0A03366g|transcript|CAGL0A03366g-T|protein_coding||c.*883A>C|||||482|,G|downstream_gene_variant|MODIFIER|CAGL0A03388g|CAGL0A03388g|transcript|CAGL0A03388g-T|protein_coding||c.*3644A>C|||||3475|,G|non_coding_transcript_exon_variant|MODIFIER|CAGL0A03355r|CAGL0A03355r|transcript|CAGL0A03355r-T|lincRNA|1/1|n.250T>G||||||  GT:AD:DP:GQ:PL  0/1:1304,239:1543:99:240,0,42733
ChrA_C_glabrata_CBS138  526966  .   T   G   810.64  PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-13.367;DP=484;ExcessHet=0.0000;FS=36.698;MLEAC=1;MLEAF=0.500;MQ=56.97;MQRankSum=-6.884;QD=2.00;ReadPosRankSum=9.343;SOR=0.040;ANN=G|downstream_gene_variant|MODIFIER|CAGL0A04851g|CAGL0A04851g|transcript|CAGL0A04851g-T|protein_coding||c.*3083T>G|||||3083|,G|intergenic_region|MODIFIER|CAGL0A04851g-CHR_END|CAGL0A04851g-CHR_END|intergenic_region|CAGL0A04851g-CHR_END|||n.526966T>G||||||    GT:AD:DP:GQ:PL  0/1:325,80:405:99:818,0,5895
ChrB_C_glabrata_CBS138  334637  .   C   T   80876.06    PASS    AC=2;AF=1.00;AN=2;BaseQRankSum=-1.727;DP=2189;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.99;MQRankSum=0.000;QD=27.11;ReadPosRankSum=-1.068;SOR=0.315;ANN=T|missense_variant|MODERATE|CAGL0B03399g|CAGL0B03399g|transcript|CAGL0B03399g-T|protein_coding|1/1|c.790C>T|p.His264Tyr|1091/5453|790/4995|264/1664||,T|upstream_gene_variant|MODIFIER|CAGL0B03355g|CAGL0B03355g|transcript|CAGL0B03355g-T|protein_coding||c.-4414G>A|||||4360|,T|downstream_gene_variant|MODIFIER|CAGL0B03377g|CAGL0B03377g|transcript|CAGL0B03377g-T|protein_coding||c.*1559C>T|||||1402|,T|downstream_gene_variant|MODIFIER|CAGL0B03421g|CAGL0B03421g|transcript|CAGL0B03421g-T|protein_coding||c.*4444G>A|||||4341|    GT:AD:DP:GQ:PL  1/1:1,2013:2014:99:80890,6011,0
ChrD_C_glabrata_CBS138  851 .   A   *,C 76.01   QD_filter   AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=-5.304;DP=161;ExcessHet=0.0000;FS=11.483;MLEAC=1,1;MLEAF=0.500,0.500;MQ=42.31;MQRankSum=-3.151;QD=0.60;ReadPosRankSum=-3.681;SOR=0.053;ANN=C|downstream_gene_variant|MODIFIER|CAGL0D00143g|CAGL0D00143g|transcript|CAGL0D00143g-T|protein_coding||c.*4326T>G|||||4326|,C|intergenic_region|MODIFIER|CHR_START-CAGL0D00143g|CHR_START-CAGL0D00143g|intergenic_region|CHR_START-CAGL0D00143g|||n.851A>C|||||| GT:AD:DP:GQ:PL  1/2:23,88,16:127:73:3125,293,73,2140,0,2177

Specifically, this is seen in ChrD, where is displays

GT:AD:DP:GQ:PL

1/2:23,88,16:127:73:3125,293,73,2140,0,2177

Is this an error or how should this be calculated? Given I was already told to do this, which only takes into account two variables:

Answer 1

[Jeremy Leipzig]

the alt of *,C is a GATK convention which means there were some reads that had a C allele and some reads that are missing this position because it is located in a larger deletion. So i think the allelic depth is 23 A, 88 missing, 16 C