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 metricsB73B14

Number of paired reads 263,964,77094,976,365
Number of paired reads 2 with signature sequence 61,512,15192,262,878

Alignment against the B73 reference genome sequencea
Align once31,121,35557,009,568
Align more than once13,306,20622,869,021
Do not align 17,084,59012,384,289

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