| Variant ID: vg0409586690 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586690 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGGCCCATTATAGGTGATGCAACACCTTGTTCCTGTGATTCTGGCCACACGAGATAGAATTCAGAGAAGAGGCTGGATCCGTTAGAAAGAGGGCTCCGAG[A/G]
GCTTTCCATCAAGTACTCACGGGCCAAAAACGGAGGTCGTATGCAGATTCGGTGGCCGTTTGAAGTCAGCAGTGTAGTAGGTGGCCGAATCGGATTCCAG
CTGGAATCCGATTCGGCCACCTACTACACTGCTGACTTCAAACGGCCACCGAATCTGCATACGACCTCCGTTTTTGGCCCGTGAGTACTTGATGGAAAGC[T/C]
CTCGGAGCCCTCTTTCTAACGGATCCAGCCTCTTCTCTGAATTCTATCTCGTGTGGCCAGAATCACAGGAACAAGGTGTTGCATCACCTATAATGGGCCT
| 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 | 35.80% | 1.70% | 31.65% | 30.91% | NA |
| All Indica | 2759 | 16.60% | 2.80% | 38.49% | 42.19% | NA |
| All Japonica | 1512 | 72.60% | 0.10% | 16.34% | 10.98% | NA |
| Aus | 269 | 21.20% | 0.00% | 43.87% | 34.94% | NA |
| Indica I | 595 | 17.50% | 2.20% | 47.73% | 32.61% | NA |
| Indica II | 465 | 11.40% | 2.80% | 26.45% | 59.35% | NA |
| Indica III | 913 | 18.50% | 3.80% | 35.93% | 41.73% | NA |
| Indica Intermediate | 786 | 16.70% | 1.90% | 41.60% | 39.82% | NA |
| Temperate Japonica | 767 | 96.90% | 0.00% | 1.83% | 1.30% | NA |
| Tropical Japonica | 504 | 33.90% | 0.20% | 39.29% | 26.59% | NA |
| Japonica Intermediate | 241 | 76.30% | 0.00% | 14.52% | 9.13% | NA |
| VI/Aromatic | 96 | 46.90% | 0.00% | 37.50% | 15.62% | NA |
| Intermediate | 90 | 37.80% | 1.10% | 36.67% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586690 | A -> DEL | N | N | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586690 | A -> G | LOC_Os04g17510.1 | upstream_gene_variant ; 1999.0bp to feature; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586690 | A -> G | LOC_Os04g17530.1 | downstream_gene_variant ; 1548.0bp to feature; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586690 | A -> G | LOC_Os04g17540.1 | downstream_gene_variant ; 4007.0bp to feature; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586690 | A -> G | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |