1. Volume 8, Issue 6, Pages 831-846 (June 2015)
Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations 
Josh Clevenger, Carolina Chavarro, Stephanie A. Pearl, Peggy Ozias-Akins, Scott A. Jackson 
Molecular Plant 
Volume 8, Issue 6, Pages (June 2015)
DOI: /j.molp
Copyright © 2015 The Author Terms and Conditions

2. Figure 1
Comparison of SNP Calls Generated by SAMtools on Alignment Files Produced by BWA-mem and Bowtie 2.
The number appearing in the overlapping portion of the Venn diagram represents the total number of concordant SNPs identified.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

3. Figure 2
Comparison of SNP Calls Generated by SAMtools, GATK, and Freebayes on Alignment Files Produced by Bowtie 2.
The number appearing in the center overlapping portion of the Venn diagram represents the total number of concordant SNPs identified.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

4. Figure 3
Characteristics of Unique (Blue) and Concordant (Red) SNP Calls, Based on a Random Subset of 5000 of Each Type.
(A) Frequency distribution of the ratio of the number of reads containing the alternate allele to those containing the reference allele at each called SNP.
(B) Frequency distribution depicting the degree of SNP position bias for each called SNP. Higher values indicate that SNPs tend to be found in certain positions of aligned reads and are therefore likely to be artifacts of the analysis.
(C) Frequency distribution of the tail position bias of each called SNP. Values on the x axis represent Z scores calculated from a Mann-Whitney U-test. Greater deviations from zero represent SNP calls systematically occurring at the ends of reads that are likely false-positives occurring as a result of misalignment.
(D) Frequency distribution of the P values describing map quality bias for each called SNP. Here, P values describe the probability that each called SNP is real and not an artifact of bad mapping quality.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

5. Figure 4
Relative Performance of Freebayes, GATK, and SAMtools on Simulated Chromosomes 1A and 1C of B. napus.
(A and B) Alignments produced by (A) BWA-mem, and (B) Bowtie 2. Common and rare classes represent true allelic SNP calls, and green segments represent SNPs that each caller failed to identify within these classes (false-negatives). Homeologous SNPs (red) represent false-positive SNP calls.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

6. Figure 5
Decision Tree Intended as a Guide for Choosing a Library Preparation Strategy for SNP Discovery Projects.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions