| Variant ID: vg0721993454 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993454 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )
TTGGTGGAATGGGCCCTATTGGGCTGAAATACACACGCCTACACTCAACACTCCCCCTCAAGATGGGCGATAAATATCTATCATGCCCATCTTGCTACAC[G/A]
AAGAAGTGCACTCTCTAGCACCTAATGCCTTCGTTAAACTATCAGCTACTTGTTCACCAGAGTTTACAAAGCCTAAGTTTAAGGTTCCCTCATCCATTCT
AGAATGGATGAGGGAACCTTAAACTTAGGCTTTGTAAACTCTGGTGAACAAGTAGCTGATAGTTTAACGAAGGCATTAGGTGCTAGAGAGTGCACTTCTT[C/T]
GTGTAGCAAGATGGGCATGATAGATATTTATCGCCCATCTTGAGGGGGAGTGTTGAGTGTAGGCGTGTGTATTTCAGCCCAATAGGGCCCATTCCACCAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.10% | 0.90% | 2.35% | 1.63% | NA |
| All Indica | 2759 | 97.20% | 1.40% | 1.30% | 0.04% | NA |
| All Japonica | 1512 | 92.50% | 0.00% | 2.45% | 5.03% | NA |
| Aus | 269 | 85.90% | 0.40% | 13.75% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.20% | 1.01% | 0.00% | NA |
| Indica II | 465 | 96.80% | 2.20% | 0.86% | 0.22% | NA |
| Indica III | 913 | 96.70% | 2.00% | 1.31% | 0.00% | NA |
| Indica Intermediate | 786 | 96.80% | 1.40% | 1.78% | 0.00% | NA |
| Temperate Japonica | 767 | 96.90% | 0.00% | 0.78% | 2.35% | NA |
| Tropical Japonica | 504 | 90.10% | 0.00% | 4.37% | 5.56% | NA |
| Japonica Intermediate | 241 | 83.80% | 0.00% | 3.73% | 12.45% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993454 | G -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:24.584; most accessible tissue: Minghui63 root, score: 47.894 | N | N | N | N |
| vg0721993454 | G -> A | LOC_Os07g36710.1 | missense_variant ; p.Ser790Leu; MODERATE | nonsynonymous_codon ; S790L | Average:24.584; most accessible tissue: Minghui63 root, score: 47.894 | unknown | unknown | TOLERATED | 1.00 |