Table 1.
A summary comparison of independent allele catalog tools developed for soybean, maize, and Arabidopsis thaliana provides details relevant to the underlying data for each tool
| Soybean | Maize | Arabidopsis | |
|---|---|---|---|
| Name | Soy1066 | MaizePanzeaAGPv3 | Arabidopsis1135 |
| Reference Genome | Wm82.a2.v1 | AGPv3 | TAIR10 |
| Number of Accessions | 1,066 | 1,208 | 1,135 |
| Genome Size | 978,495,272 | 2,067,864,162 | 119,667,750 |
| Total Variant Positions | 38,302,167 | 79,430,168 | 11,501,945 |
| Total SNP Positions | 32,524,427 | 74,306,694 | 11,462,068 |
| Total Indel Positions | 5,777,740 | N/A | 39,877 |
| Mean of Missing Data Per Accession | 3,412,030 | 40,704,160 | 1,987,800 |
| Number of Genes | 54,012 | 58,946 | 26,923 |
| Number of Genes with Only Reference Allele | 1,577 | 4,534 | 493 |
| Number of Genes with Null Alleles | 35,457 | 22,585 | 15,889 |
| Number of Modifying Variants (SNPs and Indels) | 618,501 | 1,093,495 | 1,129,470 |
| Number of Null Variants (SNPs and Indels) | 141,167 | 84,840 | 61,974 |
| Mean of Number of Allele Positions Per Gene | 40 | 62 | 129 |
| Median of Number of Allele Positions Per Gene | 22 | 43 | 91 |
| Mean of Number of Alleles Per Gene | 17 | 47 | 45 |
| Median of Number of Alleles Per Gene | 9 | 24 | 32 |
Table 1 Soybean, maize, and Arabidopsis Allele Catalog data information