| Variant ID: vg0409586692 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586692 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 232. )
GCCCATTATAGGTGATGCAACACCTTGTTCCTGTGATTCTGGCCACACGAGATAGAATTCAGAGAAGAGGCTGGATCCGTTAGAAAGAGGGCTCCGAGAG[C/A]
TTTCCATCAAGTACTCACGGGCCAAAAACGGAGGTCGTATGCAGATTCGGTGGCCGTTTGAAGTCAGCAGTGTAGTAGGTGGCCGAATCGGATTCCAGCA
TGCTGGAATCCGATTCGGCCACCTACTACACTGCTGACTTCAAACGGCCACCGAATCTGCATACGACCTCCGTTTTTGGCCCGTGAGTACTTGATGGAAA[G/T]
CTCTCGGAGCCCTCTTTCTAACGGATCCAGCCTCTTCTCTGAATTCTATCTCGTGTGGCCAGAATCACAGGAACAAGGTGTTGCATCACCTATAATGGGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.50% | 0.00% | 3.34% | 42.15% | NA |
| All Indica | 2759 | 38.10% | 0.00% | 4.71% | 57.23% | NA |
| All Japonica | 1512 | 84.70% | 0.10% | 0.40% | 14.75% | NA |
| Aus | 269 | 36.80% | 0.00% | 4.83% | 58.36% | NA |
| Indica I | 595 | 32.40% | 0.00% | 7.39% | 60.17% | NA |
| Indica II | 465 | 32.30% | 0.00% | 4.30% | 63.44% | NA |
| Indica III | 913 | 41.70% | 0.00% | 3.29% | 54.98% | NA |
| Indica Intermediate | 786 | 41.50% | 0.00% | 4.58% | 53.94% | NA |
| Temperate Japonica | 767 | 97.70% | 0.10% | 0.13% | 2.09% | NA |
| Tropical Japonica | 504 | 63.50% | 0.20% | 0.99% | 35.32% | NA |
| Japonica Intermediate | 241 | 88.00% | 0.00% | 0.00% | 12.03% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 6.25% | 10.42% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 3.33% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586692 | C -> DEL | N | N | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586692 | C -> A | LOC_Os04g17510.1 | upstream_gene_variant ; 2001.0bp to feature; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586692 | C -> A | LOC_Os04g17530.1 | downstream_gene_variant ; 1546.0bp to feature; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586692 | C -> A | LOC_Os04g17540.1 | downstream_gene_variant ; 4005.0bp to feature; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586692 | C -> A | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |