Local Assemblies of Paired-End Reduced Representation Libraries Sequenced with the Illumina Genome Analyzer in Maize

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 sequence^a
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.