Table 1: Run metrics. The numbers of paired reads 2, paired reads 2 containing the 10 bp “TGCAGGTGCA” signature sequence at their 5′ ends, and paired reads 2 aligning to the public B73RefGen_v2 reference genome sequence are indicated.

Run metrics B73 B14 Number of paired reads 2 63,964,770 94,976,365 Number of paired reads 2 with signature sequence 61,512,151 92,262,878 Alignment against the B73 reference genome sequencea     Align once 31,121,355 57,009,568 Align more than once 13,306,206 22,869,021 Do not align 17,084,590 12,384,289

aBest match to reference sequence of reads aligning uniquely or multiple times to the reference sequence with no more than 2 mismatches.