| Variant ID: vg0410079763 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10079763 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAGTCAGCAGTGTAGTAGGTGGCCGAATCGGATTCCAGCACTTGGAGGATTTGATCTTGATATCTTCTTGTTCATCCATGATGTGAGCAATGGTTGCATC[T/C]
GTGGTAGCCATGGTCACATCATCCTCCCCTTCTTCACGGAAAACCGTCCTCGGTCTTTTGGAATCATCGTCTTTTTCGCTTTGGAAGTTCGTGGATTCGA
TCGAATCCACGAACTTCCAAAGCGAAAAAGACGATGATTCCAAAAGACCGAGGACGGTTTTCCGTGAAGAAGGGGAGGATGATGTGACCATGGCTACCAC[A/G]
GATGCAACCATTGCTCACATCATGGATGAACAAGAAGATATCAAGATCAAATCCTCCAAGTGCTGGAATCCGATTCGGCCACCTACTACACTGCTGACTT
| 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 | 29.60% | 0.40% | 7.22% | 62.78% | NA |
| All Indica | 2759 | 5.00% | 0.60% | 7.47% | 86.92% | NA |
| All Japonica | 1512 | 77.20% | 0.10% | 6.88% | 15.81% | NA |
| Aus | 269 | 1.10% | 0.40% | 4.09% | 94.42% | NA |
| Indica I | 595 | 6.90% | 0.30% | 7.39% | 85.38% | NA |
| Indica II | 465 | 6.90% | 0.40% | 9.89% | 82.80% | NA |
| Indica III | 913 | 2.30% | 1.10% | 7.01% | 89.59% | NA |
| Indica Intermediate | 786 | 5.70% | 0.30% | 6.62% | 87.40% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.65% | 2.87% | NA |
| Tropical Japonica | 504 | 49.80% | 0.00% | 18.06% | 32.14% | NA |
| Japonica Intermediate | 241 | 73.40% | 0.40% | 3.32% | 22.82% | NA |
| VI/Aromatic | 96 | 51.00% | 0.00% | 15.62% | 33.33% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 5.56% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079763 | T -> C | LOC_Os04g18230.1 | synonymous_variant ; p.Thr4Thr; LOW | synonymous_codon | Average:12.886; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0410079763 | T -> DEL | LOC_Os04g18230.1 | N | frameshift_variant | Average:12.886; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |