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Table 2 SNP calls remaining after sequential filtration of downsampling experiment data

From: High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra

Sequential filtration Exp1 Exp2
None 5090 1616
After F1a 4500 1449
After F2b 4055 (2304)c 1343 (545)c
After MD filter >20%d 550 (347)c 320 (132)c
After MD filter >10%d 113 (61)c 63 (20)c
After MD filter ≥5%d 20 (6)c 10 (3)c
  1. aRemoval of markers with >1 SNP in the same sequence
  2. bRemoval of markers in which the SNP occurs in the first 9 bases of sequence
  3. cSubset of markers meeting criterion of chi-square value ≤ 20
  4. dRemoval of markers in which >20%, >10% or ≥5% of 217 individuals have missing data, as indicated