Show presence of known mutation in RNA-seq data
For counting reads I use mpileup, e.g. samtools mpileup --reference hg38.fa -r Chr10:18000-45500 input.bam, which will give base-resolution coverage for a BAM file.

I've written my own script to process mpileup output and make it easier to understand. By default it reports read coverage as a proportion of total coverage, but this can be modified by using the -counts command line argument:

$ samtools mpileup -r tig00018708_tig00000379:210665-240664:2107-2130 --reference trimMmerged_tig00018708_other.fasta local_Sampled_50M_vs_trimMmerged_tig00018708_other.bam  | /bioinf/scripts/readstomper.pl -counts

[mpileup] 1 samples in 1 input files
&lt;mpileup&gt; Set max per-file depth to 8000
Assembly,Position,Coverage,ref,cR,pR,A,C,G,T,d,i,InsMode
tig00018708_tig00000379:210665-240664,2107,10,C,10,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2108,11,G,11,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2109,11,T,11,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2110,11,T,11,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2111,12,G,12,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2112,14,G,14,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2113,13,C,13,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2114,13,G,13,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2115,13,C,2,0.15,0,0,0,11,0,0
tig00018708_tig00000379:210665-240664,2116,15,T,14,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2117,15,G,14,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2118,18,A,17,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2119,19,T,18,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2120,19,C,18,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2121,18,A,7,0.41,0,0,10,0,0,0
tig00018708_tig00000379:210665-240664,2122,18,G,18,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2123,18,T,18,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2124,18,C,18,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2125,18,C,9,0.50,0,0,0,9,0,0
tig00018708_tig00000379:210665-240664,2126,18,C,14,0.78,2,0,1,1,0,0
tig00018708_tig00000379:210665-240664,2127,18,C,18,1.00,0,0,0,0,0,0
tig00018708_tig00000379:210665-240664,2128,18,T,15,0.83,0,0,3,0,0,0
tig00018708_tig00000379:210665-240664,2129,17,A,13,0.76,0,0,4,0,0,0
tig00018708_tig00000379:210665-240664,2130,16,A,9,0.56,0,6,1,0,0,0


Note that only non-reference coverage is reported in the A/C/G/T/d/i columns. I have found that this makes it easier for subsequent data analysis, but your mileage may vary.