| Variant ID: vg0430654813 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30654813 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )
CTAAACTATCCAAGTTCAACAGATTACACTAGGGTGAGACTAATCACGGTGAATCTGGTTGACCGCCCATAACCGCGGGCACGGCTATTCGAATAGTTTT[A/G]
CTCTGATCAGAGGTGTACAACTGTACCCACAAGACACAGCCCCACGACACGTTTCCGTGTGCCGACATGCCACCACGACATACCGGAAAGAGGCCGTGAC
GTCACGGCCTCTTTCCGGTATGTCGTGGTGGCATGTCGGCACACGGAAACGTGTCGTGGGGCTGTGTCTTGTGGGTACAGTTGTACACCTCTGATCAGAG[T/C]
AAAACTATTCGAATAGCCGTGCCCGCGGTTATGGGCGGTCAACCAGATTCACCGTGATTAGTCTCACCCTAGTGTAATCTGTTGAACTTGGATAGTTTAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.80% | 0.20% | 29.07% | 56.94% | NA |
| All Indica | 2759 | 2.30% | 0.00% | 41.36% | 56.32% | NA |
| All Japonica | 1512 | 37.50% | 0.60% | 6.28% | 55.62% | NA |
| Aus | 269 | 0.40% | 0.00% | 37.55% | 62.08% | NA |
| Indica I | 595 | 0.80% | 0.00% | 21.68% | 77.48% | NA |
| Indica II | 465 | 4.50% | 0.00% | 46.24% | 49.25% | NA |
| Indica III | 913 | 2.00% | 0.00% | 58.16% | 39.87% | NA |
| Indica Intermediate | 786 | 2.50% | 0.00% | 33.84% | 63.61% | NA |
| Temperate Japonica | 767 | 63.20% | 0.30% | 1.17% | 35.33% | NA |
| Tropical Japonica | 504 | 6.30% | 0.40% | 10.91% | 82.34% | NA |
| Japonica Intermediate | 241 | 20.70% | 2.10% | 12.86% | 64.32% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 14.58% | 82.29% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 25.56% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430654813 | A -> DEL | N | N | silent_mutation | Average:6.435; most accessible tissue: Minghui63 flag leaf, score: 13.491 | N | N | N | N |
| vg0430654813 | A -> G | LOC_Os04g51720.1 | downstream_gene_variant ; 2415.0bp to feature; MODIFIER | silent_mutation | Average:6.435; most accessible tissue: Minghui63 flag leaf, score: 13.491 | N | N | N | N |
| vg0430654813 | A -> G | LOC_Os04g51740.1 | downstream_gene_variant ; 2566.0bp to feature; MODIFIER | silent_mutation | Average:6.435; most accessible tissue: Minghui63 flag leaf, score: 13.491 | N | N | N | N |
| vg0430654813 | A -> G | LOC_Os04g51730.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.435; most accessible tissue: Minghui63 flag leaf, score: 13.491 | N | N | N | N |