Table 2.

Differential isoform usage between Pru and RH strains

Gene	Pru	RH
TGME49_008740	(0,0):3272,(0,1):62,(1,0):14,(1,1):275	(0,0):9355,(0,1):99,(1,0):73,(1,1):799
TGME49_112660	(0,0):580,(0,1):2,(1,0):4,(1,1):68	(0,0):667,(0,1):23,(1,1):74
TGME49_078510	(0,0):2647,(0,1):15,(1,0):15,(1,1):178	(0,0):4612,(0,1):18,(1,0):5,(1,1):225
TGME49_097470	(0,0):1648,(0,1):12,(1,0):22,(1,1):140	(0,0):3796,(0,1):19,(1,1):297

(0,0):x indicates x reads align to both isoforms but are not used in support of either isoform for a variety of reasons including reads aligning to exons far removed from the spliced site, (0,1):x, x reads support the second isoform but not the first, (1,0):x indicate x reads support the first isoform and not the second (1,1):x, x reads supporting both isoforms. Missing values for RH indicate the absence of reads supporting the alternative isoform. The gene descriptions are shown in Table 1.