Table 5 Statistics of contigs and single nucleotide polymorphisms obtained for two restriction enzyme combinations (PM = PstI + MspI; HH = HinfI + HpyCH4IV) in combined runs of 12 Arabidopsis and 12 rice samples
ArabidopsisRice
StatisticPMHHPMHH
Contig statistic
 Total contigs10,49842,35528,61136,808
 Mean contig length (SD) in bp243 (18)242 (20)239 (18)238 (19)
 Total reads6,334,5455,431,3305,514,7073,547,509
 Mean reads/contig603.4128.2192.796.4
 Mean reads/contig/sample50.310.716.18.0
 Contigs with SNP0 (%)239 (2.3)473 (1.1)1308 (4.6)852 (2.3)
 Contigs with SNP0 + SNP1 (%)368 (3.5)1623 (3.8)1960 (6.9)1900 (5.2)
 Contigs with SNP0 + SNP1 + SNP2 (%)453 (4.3)2915 (6.9)2319 (8.1)2834 (7.7)
 Contigs with SNPwt (%)672 (6.4)5405 (12.8)3687 (12.9)5096 (13.8)
SNP statistic
 Total SNPs134311,489788611,526
 Total reads350,269925,4681,412,2331,052,072
 Mean reads/SNP260.880.6179.191.3
 Mean reads/SNP/sample21.76.714.97.6
 SNP0 (%)423 (31.5)1122 (9.8)2325 (29.5)1995 (17.3)
 SNP0 + SNP1 (%)688 (51.2)3417 (29.7)3823 (48.5)4216 (36.6)
 SNP0 + SNP1 + SNP2 (%)884 (65.8)6168 (53.7)4753 (60.3)6261 (54.3)
  • The percent of the total contigs or total SNPs (single nucleotide polymorphisms) is shown in parenthesis. SNP0, SNPs having no missing observations across the 12 samples; SNP1, SNPs having 8.3% observations missing (or absent in one of the 12 samples); SNP2, SNPs having 16.7% observations missing (or absent in two of the 12 samples); SNPwt, SNPs with or without missing observations across the 12 samples.