Effects of a wide range of dietary forage-to-concentrate ratios on nutrient utilization and hepatic transcriptional profiles in limit-fed Holstein heifers

Table 4 Statistics for RNA-Seq reads from liver biopsy, and alignment information with Tophat^a (group means)

Mapping summary	Forage levels (% of diet DM)
Mapping summary	20	40	60	80
Total reads (raw reads)	45,397,012	44,701,037	43,415,394	45,897,090
Clean reads	44,679,767	43,983,934	42,714,824	45,155,970
Statistic for clean reads: Q20^b	99.79%	99.83%	99.83%	99.83%
Statistic for clean reads: Q30^c	92.88%	92.94%	92.80%	92.80%
Statistic for clean reads: GC content	44.17%	45.00%	44.00%	44.00%
Statistic for clean reads: Seq-Dupl-level^d	85.18%	83.91%	84.30%	82.52%
Mapping rate	89.72%	90.20%	90.03%	89.97%
Total mapped reads	40,109,810	39,668,475	38,458,347	40,641,575
Multiple mapped reads	2,938,690	2,958,931	2,849,620	3,070,914
Unique mapped reads	37,171,120	36,709,544	35,608,727	37,570,661
Junction mapped reads	19,339,604	18,902,568	18,610,456	19,784,290
Statistic for clean reads: error rate	0.29%	0.30%	0.30%	0.31%

^aBovine genome UMD3.1 was used for the alignment
^bQ20, the proportion of bases with a phred base-quality score > 20; i.e., the proportion of read bases with an error rate less than 1%
^cQ30, the proportion of bases with a phred base-quality score > 30; i.e., the proportion of read bases with an error rate less than 0.1%
^dSeq-Dupl-level, sequence duplication level

ISSN: 1471-2164