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Table 1 Error rates calculated by comparing four sets of duplicated samples. D1/D2: ratio of reads from Duplicate 1 to Duplicate 2. Locus misassignment rate: the percentage of unidentified loci, calculated by dividing the number of loci found only in one of the duplicates by the total number of loci in each sample. Allele misassignment rate: the percentage of mismmatches between the IUPAC consensus sequences between homologous loci from each pair of duplicates. SNP error rate 1: the percentage of different SNPs called in each of the duplicated samples using either 10178 SNPs. Shared SNP error rate: the percentage of different SNPs called in each of the duplicated samples after excluding missing data between duplicate samples

From: Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

 

F06-B02

A12-F12

H11-G06

G02-D01

MEAN

SD

Reads (D1/D2)

0.19

3.54

1.29

1.380

  

Coverage

8.93/11.20

15.95/10.22

8.05/10.51

7.62/8.54

  

Locus misassignment rate

0.10

0.08

0.04

0.04

0.07

0.031

Allele misassignment rate

0.08

0.06

0.07

0.05

0.07

0.01

SNP error rate 1

0.15

0.12

0.05

0.07

0.10

0.04

Shared SNP error rate

0.006

0.004

0.007

0.004

0.005

0.002