# SNP Data Analysis Report Template

## Basic Information
- **Dataset Name/Source:** ___________________________
- **Analysis Date:** ____/____/____
- **Analyst:** ___________________________
- **Original Number of Samples:** ______
- **Original Number of SNPs:** ______

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## Data Quality Control (QC)

### Sample QC
- **Filtering Criteria:**  
  - Missing rate > ______
  - Heterozygosity rate > ______
- **Number of Samples After QC:** ______
- **Number of SNPs After QC:** ______

### SNP QC
- **Filtering Criteria:**  
  - Missing rate > ______
  - Heterozygosity rate < ______
  - Heterozygosity rate > ______
  - -log(p) for Hardy-Weinberg equilibrium (HWE) > ______
- **Number of Samples After QC:** ______
- **Number of SNPs After QC:** ______

### SNP Density Summary
- **Reference Genome:** ___________________________
- **Number of Chromosomes:** ______
- **Total Genome Length (bp):** ______
- **Number of SNPs After QC:** ______
- **Average SNP Spacing (bp):** ______
- **Number of SNPs per 1000 bp:** ______

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## Dataset for Downstream Analysis

- **Final Number of Samples:** ______
- **Final Number of SNPs:** ______

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## Population Structure Analysis

### Principal Component Analysis (PCA)
- **Variance Explained by Top PCs (PC1 ~ PCn):** ___________________________

### Discriminant Analysis of Principal Components (DAPC)
- **Optimal Number of Groups (K) and Criterion:** K = ______ (e.g., BIC/other criteria)
- **Sample Size per Group:**
  - Group 1: ______
  - Group 2: ______
  - Group 3: ______
  - Group 4: ______
  - ...
- **Group Centroids on Discriminant Axes:**  
  - Discriminant Function 1: Group 1 ______, Group 2 ______, Group 3 ______, Group 4 ______
  - Discriminant Function 2: Group 1 ______, Group 2 ______, Group 3 ______, Group 4 ______

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## Genetic Diversity

- **Average Missing Rate (%):** ______
- **Average Minor Allele Frequency (MAF):** ______
- **Average Nucleotide Diversity (π):** ______
- **Average Expected Heterozygosity (He) per Group:**
  - Group 1: ______
  - Group 2: ______
  - Group 3: ______
  - Group 4: ______
- **Average Unbiased Pi per Group:**
  - Group 1: ______
  - Group 2: ______
  - Group 3: ______
  - Group 4: ______
- **Number of Exclusive Alleles per Group:**
  - Group 1: ______
  - Group 2: ______
  - Group 3: ______
  - Group 4: ______
- **Number of Fixed Alleles per Group:**
  - Group 1: ______
  - Group 2: ______
  - Group 3: ______
  - Group 4: ______

### Genetic Distance (Between Groups)
- Group 1 – Group 2: ______
- Group 1 – Group 3: ______
- Group 1 – Group 4: ______
- Group 2 – Group 3: ______
- Group 2 – Group 4: ______
- Group 3 – Group 4: ______

### Analysis of Molecular Variance (AMOVA)
- **Among Groups Variance (%):** ______ (p-value: ______)
- **Among Individuals Within Groups Variance (%):** ______ (p-value: ______)
- **Within Individuals Variance (%):** ______ (p-value: ______)

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## Selection Sweep Analysis

### pcadapt (PCA-based Genome Scan)
- **Number of Significant SNPs:** ______
- **Threshold / FDR / α:** ______
- **Chromosomes Involved:** ______

### OutFLANK (Fst-based Genome Scan)
- **Number of Significant SNPs:** ______
- **Threshold / FDR / α:** ______
- **Chromosomes Involved:** ______

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## Core Collection

### Core Sample Set
- **Number of Core Samples:** ______
- **Proportion of Total Samples (%):** ______
- **Coverage (%):** ______

### Core SNP Set
- **Number of Core SNPs:** ______
- **Proportion of Total SNPs (%):** ______

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## Notes / Additional Remarks

- _________________________________________________________________

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> **Instructions:**  
> This template can be customized according to your laboratory requirements.