Table 2.

RNA-seq analysis of ‘Alamo’ and ‘Dacotah’ used for variant detection and gene expression analysis. One sample of ‘Alamo’ and one sample of ‘Dacotah’ were sequenced at a deep coverage (36X and 20X, respectively) and were used for variant detection. Three biological replicates of ‘Alamo’ and ‘Dacotah’ were used for gene expression analysis and were sequenced between 3.7X and 5.2X coverage

Sample	Sequencing	Initial reads	Trimmed reads	Mapped reads	% Reads mapped
Alamo	101 bp-PE	221,647,550	216,244,584	180,996,166	84.35
Dacotah	101 bp-PE	125,257,298	121,958,884	99,283,683	82.03
Alamo- 1	50 bp-PE	56,036,894	54,211,026	52,494,171	96
Alamo- 2	50 bp-PE	45,931,626	44,044,084	42,657,586	96
Alamo- 3	50 bp-PE	58,312,466	55,472,698	53,590,453	96
Dacotah- 1	50 bp-PE	59,434,186	56,774,376	54,489,840	96
Dacotah- 2	50 bp-PE	48,408,374	46,266,102	44,525,787	96
Dacotah- 3	50 bp-PE	63,304,978	61,060,688	58,815,617	96