bam-readcount : Reference_base is not the base with highest count

Question

[AB]

Hi,

I recently ran bam-readcount on my bamfile and I noticed something weird about my result

chr1    201334382   G   58077   =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  A:57989:238.35:35.90:0.01:34667:23322:0.51:0.01:43.91:34670:0.52:122.12:0.49    C:8:255.00:33.00:0.00:6:2:0.37:0.02:56.38:6:0.76:120.62:0.62    G:61:242.61:34.13:0.00:41:20:0.37:0.01:20.82:41:0.77:116.07:0.60    T:17:255.00:35.24:0.00:15:2:0.25:0.02:50.18:15:0.76:117.06:0.69 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  -G:2:255.00:0.00:0.00:1:1:0.68:0.02:21.00:1:0.38:124.50:0.34

Clearly, A has the highest base count (57989). Then why is the reference base being reported as G?

[GenoMax]

Reference base is from your reference and is being reported as is, no?

Answer 1

[iraun]

In the bam-readcount GitHub repository, you can clearly understand the output format:

chr position    reference_base  depth   base:count:avg_mapping_quality:avg_basequality:avg_se_mapping_quality:num_plus_strand:num_minus_strand:avg_pos_as_fraction:avg_num_mismatches_as_fraction:avg_sum_mismatch_qualities:num_q2_containing_reads:avg_distance_to_q2_start_in_q2_reads:avg_clipped_length:avg_distance_to_effective_3p_end   ...

So, in your case, a G is reported because you have a G in your reference genome.

[AB]

OK. So this basically means that the genotype is homozygous for the alternative allele ?