| Variant ID: vg0410079712 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10079712 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGTACTCACGGGCCGAAAACGGAGGTCGTATGCAGATTCGGCAGCCGTTTGAAGTCAGCAGTGTAGTAGGTGGCCGAATCGGATTCCAGCACTTGGAGGA[T/C]
TTGATCTTGATATCTTCTTGTTCATCCATGATGTGAGCAATGGTTGCATCTGTGGTAGCCATGGTCACATCATCCTCCCCTTCTTCACGGAAAACCGTCC
GGACGGTTTTCCGTGAAGAAGGGGAGGATGATGTGACCATGGCTACCACAGATGCAACCATTGCTCACATCATGGATGAACAAGAAGATATCAAGATCAA[A/G]
TCCTCCAAGTGCTGGAATCCGATTCGGCCACCTACTACACTGCTGACTTCAAACGGCTGCCGAATCTGCATACGACCTCCGTTTTCGGCCCGTGAGTACT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.90% | 0.30% | 18.05% | 49.81% | NA |
| All Indica | 2759 | 19.80% | 0.00% | 23.34% | 56.87% | NA |
| All Japonica | 1512 | 60.90% | 0.80% | 6.35% | 31.94% | NA |
| Aus | 269 | 3.30% | 0.00% | 19.33% | 77.32% | NA |
| Indica I | 595 | 25.00% | 0.00% | 25.38% | 49.58% | NA |
| Indica II | 465 | 25.20% | 0.00% | 13.12% | 61.72% | NA |
| Indica III | 913 | 13.10% | 0.00% | 28.26% | 58.60% | NA |
| Indica Intermediate | 786 | 20.40% | 0.00% | 22.14% | 57.51% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.26% | 3.91% | NA |
| Tropical Japonica | 504 | 6.20% | 0.00% | 17.46% | 76.39% | NA |
| Japonica Intermediate | 241 | 64.30% | 5.00% | 2.49% | 28.22% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 42.71% | 56.25% | NA |
| Intermediate | 90 | 33.30% | 0.00% | 22.22% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079712 | T -> C | LOC_Os04g18230.1 | synonymous_variant ; p.Lys21Lys; LOW | synonymous_codon | Average:9.199; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0410079712 | T -> DEL | LOC_Os04g18230.1 | N | frameshift_variant | Average:9.199; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |