Table 2.

Gene and Transcript Level Comparison to Manual Annotations

	Gene Sn	Level Sp	Transcript Sn	Level Sp	No exons unpaired	1 exon unpaired	2 exons unpaired
chr13	0.82	0.39	0.71	0.42	35.6%	16.5%	10.7%
chr14	0.83	0.42	0.72	0.35	26.2%	17.5%	11.9%
chr20	0.85	0.46	0.64	0.45	32.2%	17.8%	11.6%
chr6	0.81	0.38	0.74	0.29	36.7%	16.3%	11.9%

Genes are compared according to the genomic extent, from which we draw gene pairs. At the transcript level, variants from either gene in the gene pairs are paired up according to the best transcript alignment. A transcript is considered as found if there is an alignment with a predicted transcript that has no better alignment with the other annotated transcripts. The sensitivity (Sn) is calculated as the number of paired-up annotated transcripts over the total number of annotated transcripts, and the specificity (Sp) is calculated by using the same numerator and the total number of predicted transcripts as denominator. We also give the percentage of the transcript pairs that have zero, one, and two exons unpaired.