Table 1.

Adjustable parameters for model scoring and read island assembly

Parameter	Default value
Maximum homolog count	3
Acceptable intron donor-acceptor pairs	GT-AG, GC-AG, AT-AC
Minimum intron length	10
Maximum intron length	2000
Minimum protein length	150 amino acids
Low median coverage cutoff	10
Low coverage penalty factor	0.6
Acceptable range of exon coverage depth	0.15 to 3 × transcript median depth
Maximum length of low coverage run	10
Low coverage run threshold	0.05 × transcript mean depth
Maximum N count per transcript	8
Threshold score for “Matches RNA-Seq data” status	0.5
Selection pseudoscore	0.0001
Read island minimum cover depth	3
Read island minimum length	100