Hello folks,

I am trying see the allelic expression from RNA seq data for that I have used heterozygous SNPs from VCF file, using GATK asereadcounter got the SNPs count problem I am confused with a genes SNPs showing both biallelic count and monoallelic count any one suggest what will be the issue below giving some examples

     ID          Chromosome SNP Ref Alt gene_name
ENSMUSG00000033845  1   4774188 12  0   Mrpl15
ENSMUSG00000033845  1   4774538 10  0   Mrpl15
ENSMUSG00000033845  1   4775069 10  0   Mrpl15
ENSMUSG00000033845  1   4775803 10  0   Mrpl15
ENSMUSG00000033845  1   4776734 300 203 Mrpl15
ENSMUSG00000033845  1   4781549 2   8   Mrpl15
ENSMUSG00000033845  1   4782730 365 241 Mrpl15
ENSMUSG00000033845  1   4785703 122 136 Mrpl15
ENSMUSG00000033813  1   4857943 387 370 Tcea1
ENSMUSG00000033813  1   4896452 37  5   Tcea1
ENSMUSG00000033813  1   4896518 78  5   Tcea1
ENSMUSG00000033813  1   4897736 18  0   Tcea1
ENSMUSG00000033813  1   4897745 16  0   Tcea1
ENSMUSG00000033793  1   5095686 0   373 Atp6v1h
ENSMUSG00000033793  1   5124338 0   395 Atp6v1h
ENSMUSG00000033793  1   5162288 50  69  Atp6v1h
ENSMUSG00000033793  1   5162341 34  45  Atp6v1h
ENSMUSG00000033793  1   5162347 26  42  Atp6v1h
ENSMUSG00000046101  1   9941079 0   10  6030422M02Rik
ENSMUSG00000046101  1   9942048 9   13  6030422M02Rik
ENSMUSG00000036850  2   24974162    51  101 Mrpl41
ENSMUSG00000036850  2   24974614    0   482 Mrpl41
ENSMUSG00000036850  2   24974997    7   301 Mrpl41
ENSMUSG00000003131  9   45965680    0   88  Pafah1b2
ENSMUSG00000003131  9   45965880    0   163 Pafah1b2
ENSMUSG00000003131  9   45966221    93  48  Pafah1b2
ENSMUSG00000003131  9   45966516    108 106 Pafah1b2
ENSMUSG00000003131  9   45966539    139 101 Pafah1b2
ENSMUSG00000003131  9   45966968    0   332 Pafah1b2
ENSMUSG00000003131  9   45967403    0   240 Pafah1b2
ENSMUSG00000003131  9   45967446    0   296 Pafah1b2
ENSMUSG00000003131  9   45967547    3   207 Pafah1b2
ENSMUSG00000003131  9   45967758    0   36  Pafah1b2

Thank you