Molecular Vision: Brooks, Mol Vis 2011; 17:3034-3054. Table 3

Table 3. Summary of Illumina base calling and alignments

Genotype	WT	WT	WT	Nrl^−/−	Nrl^−/−	Nrl^−/−
	Sample 1	Sample 2	Sample 3	Sample 1	Sample 2	Sample 3
Total reads	35,872,080	41,785,800	49,076,400	46,689,240	48,480,240	48,656,040
PF Reads	29,603,280	33,251,160	37,642,800	36,472,800	37,119,960	36,823,320
	82.7%	79.7%	76.9%	78.2%	76.7%	75.8%
BWA alignments	24,992,271	27,922,997	32,085,799	30,960,565	31,374,578	31,257,335
TopHat alignments	30,769,939	34,177,120	39,222,596	38,289,469	38,744,790	38,593,533

Each of the 3 week old WT and Nrl^−/− retina sample was sequenced on a separate lane of the Illumina GAIIx flow cell to obtain 35 to 49 million raw reads. Over 75% of the raw reads passed Illumina’s read chastity threshold to yield 29 to 37 million usable PF reads. TopHat mapping always gave significantly more alignments than BWA because of its ability to map across the splice junctions. A relatively smaller numbers of reads and alignments for WT samples 1 and 2 are not a matter of concern as FPKM normalization was used to assess the transcript isoform expression. WT=wild type. PF=pass filter