| Variant ID: vg0721993517 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 21993517 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 340. )
TGGGCGATAAATATCTATCATGCCCATCTTGCTACACGAAGAAGTGCACTCTCTAGCACCTAATGCCTTCGTTAAACTATCAGCTACTTGTTCACCAGAG[T/A]
TTACAAAGCCTAAGTTTAAGGTTCCCTCATCCATTCTCTCTTTAATAAAGAAGCGATCTATTTCCACATGCTTCGTTCGATCATGCTGGACTGGATTGTT
AACAATCCAGTCCAGCATGATCGAACGAAGCATGTGGAAATAGATCGCTTCTTTATTAAAGAGAGAATGGATGAGGGAACCTTAAACTTAGGCTTTGTAA[A/T]
CTCTGGTGAACAAGTAGCTGATAGTTTAACGAAGGCATTAGGTGCTAGAGAGTGCACTTCTTCGTGTAGCAAGATGGGCATGATAGATATTTATCGCCCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.00% | 0.30% | 19.38% | 21.33% | NA |
| All Indica | 2759 | 43.60% | 0.50% | 24.10% | 31.79% | NA |
| All Japonica | 1512 | 88.40% | 0.00% | 3.90% | 7.74% | NA |
| Aus | 269 | 40.90% | 0.40% | 56.51% | 2.23% | NA |
| Indica I | 595 | 27.20% | 0.50% | 12.61% | 59.66% | NA |
| Indica II | 465 | 42.40% | 0.00% | 21.72% | 35.91% | NA |
| Indica III | 913 | 53.30% | 0.30% | 35.38% | 10.95% | NA |
| Indica Intermediate | 786 | 45.50% | 0.90% | 21.12% | 32.44% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.13% | 3.39% | NA |
| Tropical Japonica | 504 | 79.20% | 0.00% | 10.52% | 10.32% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 2.07% | 16.18% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 21.88% | 1.04% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 21.11% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993517 | T -> DEL | LOC_Os07g36710.1 | N | frameshift_variant | Average:7.589; most accessible tissue: Callus, score: 32.482 | N | N | N | N |
| vg0721993517 | T -> A | LOC_Os07g36710.1 | missense_variant ; p.Asn769Ile; MODERATE | nonsynonymous_codon | Average:7.589; most accessible tissue: Callus, score: 32.482 | unknown | unknown | TOLERATED | 0.08 |