| Variant ID: vg0319757125 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757125 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAGAACCATGGTTGTTGGTGGTATCATCATCATTAGTATTGCTAGTGTTGTTGTCTGCATTGCGTCCATCTTCTTGGGGCAGGAACTCTTGATGCACAAC[A/T]
GAAGATCCGGTGATCTGAAGTGGCTCAGTGCGCTGTCTTTGGTTACCACATGGAAATACTGGGATGTTGACAATCCTCCTCTTGCAGTTCGTCATCCGAT
ATCGGATGACGAACTGCAAGAGGAGGATTGTCAACATCCCAGTATTTCCATGTGGTAACCAAAGACAGCGCACTGAGCCACTTCAGATCACCGGATCTTC[T/A]
GTTGTGCATCAAGAGTTCCTGCCCCAAGAAGATGGACGCAATGCAGACAACAACACTAGCAATACTAATGATGATGATACCACCAACAACCATGGTTCTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.40% | 0.20% | 3.62% | 60.83% | NA |
| All Indica | 2759 | 9.00% | 0.30% | 4.53% | 86.23% | NA |
| All Japonica | 1512 | 83.70% | 0.00% | 2.45% | 13.89% | NA |
| Aus | 269 | 12.60% | 0.40% | 0.37% | 86.62% | NA |
| Indica I | 595 | 5.20% | 0.20% | 2.86% | 91.76% | NA |
| Indica II | 465 | 8.00% | 0.00% | 2.80% | 89.25% | NA |
| Indica III | 913 | 11.20% | 0.20% | 6.90% | 81.71% | NA |
| Indica Intermediate | 786 | 9.90% | 0.50% | 4.07% | 85.50% | NA |
| Temperate Japonica | 767 | 94.10% | 0.00% | 0.39% | 5.48% | NA |
| Tropical Japonica | 504 | 66.50% | 0.00% | 5.16% | 28.37% | NA |
| Japonica Intermediate | 241 | 86.30% | 0.00% | 3.32% | 10.37% | NA |
| VI/Aromatic | 96 | 78.10% | 1.00% | 1.04% | 19.79% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 7.78% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757125 | A -> T | LOC_Os03g35670.1 | synonymous_variant ; p.Ser633Ser; LOW | synonymous_codon | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0319757125 | A -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |