| Variant ID: vg0409586681 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586681 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CAAGCCCATAGGCCCATTATAGGTGATGCAACACCTTGTTCCTGTGATTCTGGCCACACGAGATAGAATTCAGAGAAGAGGCTGGATCCGTTAGAAAGAG[G/C]
GCTCCGAGAGCTTTCCATCAAGTACTCACGGGCCAAAAACGGAGGTCGTATGCAGATTCGGTGGCCGTTTGAAGTCAGCAGTGTAGTAGGTGGCCGAATC
GATTCGGCCACCTACTACACTGCTGACTTCAAACGGCCACCGAATCTGCATACGACCTCCGTTTTTGGCCCGTGAGTACTTGATGGAAAGCTCTCGGAGC[C/G]
CTCTTTCTAACGGATCCAGCCTCTTCTCTGAATTCTATCTCGTGTGGCCAGAATCACAGGAACAAGGTGTTGCATCACCTATAATGGGCCTATGGGCTTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.60% | 0.10% | 3.89% | 41.39% | NA |
| All Indica | 2759 | 38.40% | 0.00% | 4.93% | 56.65% | NA |
| All Japonica | 1512 | 84.30% | 0.20% | 1.12% | 14.35% | NA |
| Aus | 269 | 38.30% | 0.00% | 3.35% | 58.36% | NA |
| Indica I | 595 | 33.10% | 0.00% | 6.39% | 60.50% | NA |
| Indica II | 465 | 32.00% | 0.00% | 4.73% | 63.23% | NA |
| Indica III | 913 | 42.30% | 0.00% | 3.94% | 53.78% | NA |
| Indica Intermediate | 786 | 41.70% | 0.00% | 5.09% | 53.18% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.26% | 1.96% | NA |
| Tropical Japonica | 504 | 62.30% | 0.60% | 2.18% | 34.92% | NA |
| Japonica Intermediate | 241 | 87.60% | 0.00% | 1.66% | 10.79% | NA |
| VI/Aromatic | 96 | 84.40% | 1.00% | 14.58% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 8.89% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586681 | G -> C | LOC_Os04g17510.1 | upstream_gene_variant ; 1990.0bp to feature; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586681 | G -> C | LOC_Os04g17530.1 | downstream_gene_variant ; 1557.0bp to feature; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586681 | G -> C | LOC_Os04g17540.1 | downstream_gene_variant ; 4016.0bp to feature; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586681 | G -> C | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0409586681 | G -> DEL | N | N | silent_mutation | Average:16.091; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |