SaltxNut

Diagnostics

• Called SNPs to identify outliers

  • missing 90% of SNP data: 37, 45, 63, 186, 254, 261, 336
  • Mis-ID'd: 37, 323, 335
  • high pairwise error: 39, 67

• Library sizes

  • smaller than 5 M: 45, 63, 254, 261, 336; 186 is smaller than 7 M

• PCA

  • outliers: 37, 63, 254, 261, 323, 335, 336 (slight outliers: 39, 45, 67)
    • all 5 that have small library sizes (below 5 M.)
    • all 3 that are Mis'ID'd
    • 2 with high pairwise error

• Dendrogram

  • If cut height is 300, outliers: 37, 45, 63, 186, 254, 261, 323, 336
    • other possible outlier: 56 RHA 373 highsalt
    • does not include #39, 67, 335 (though 67 still a slight outlier)

Summary:

• Removing 3 mislabelled samples, 6 with library sizes smaller than 7 M - 8 of these are outliers on dendrogram
  • 37 mislabelled, dendrogram outlier; also PCA outlier
  • 45 library size smaller than 5 M, dendrogram oulier
  • 63 library size smaller than 5 M, dendrogram + PCA outlier
  • 186 library size smaller than 7 M, dendrogram outlier
  • 254 library size smaller than 5 M, dendrogram + PCA outlier
  • 261 library size smaller than 5 M, dendrogram + PCA outlier
  • 323 mislabelled, dendrogram outlier
  • 335 mislabelled, PCA outlier
  • 336 library size smaller than 5 M, dendrogram + PCA outlier
• Other possibilies (left in)
  • 39 high SNP pairwise error, slight PCA outlier
  • 56 dendrogram outlier
  • 67 high SNP pairwise error, slight PCA outlier
  • 224 slight dendrogram outlier