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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
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BMC Genomics

ISSN: 1471-2164

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