| Variant ID: vg0319757143 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757143 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 277. )
TGGTATCATCATCATTAGTATTGCTAGTGTTGTTGTCTGCATTGCGTCCATCTTCTTGGGGCAGGAACTCTTGATGCACAACAGAAGATCCGGTGATCTG[A/T]
AGTGGCTCAGTGCGCTGTCTTTGGTTACCACATGGAAATACTGGGATGTTGACAATCCTCCTCTTGCAGTTCGTCATCCGATTATGCTCACTTTCGAGTT
AACTCGAAAGTGAGCATAATCGGATGACGAACTGCAAGAGGAGGATTGTCAACATCCCAGTATTTCCATGTGGTAACCAAAGACAGCGCACTGAGCCACT[T/A]
CAGATCACCGGATCTTCTGTTGTGCATCAAGAGTTCCTGCCCCAAGAAGATGGACGCAATGCAGACAACAACACTAGCAATACTAATGATGATGATACCA
| 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 | 33.60% | 0.60% | 3.60% | 62.25% | NA |
| All Indica | 2759 | 6.00% | 0.90% | 4.17% | 88.91% | NA |
| All Japonica | 1512 | 83.50% | 0.00% | 3.17% | 13.29% | NA |
| Aus | 269 | 13.00% | 0.00% | 0.74% | 86.25% | NA |
| Indica I | 595 | 4.40% | 0.00% | 2.18% | 93.45% | NA |
| Indica II | 465 | 5.20% | 0.90% | 3.44% | 90.54% | NA |
| Indica III | 913 | 6.00% | 2.10% | 6.13% | 85.76% | NA |
| Indica Intermediate | 786 | 7.60% | 0.40% | 3.82% | 88.17% | NA |
| Temperate Japonica | 767 | 94.80% | 0.00% | 0.52% | 4.69% | NA |
| Tropical Japonica | 504 | 65.70% | 0.00% | 6.35% | 27.98% | NA |
| Japonica Intermediate | 241 | 85.10% | 0.00% | 4.98% | 9.96% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 5.56% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757143 | A -> T | LOC_Os03g35670.1 | synonymous_variant ; p.Leu627Leu; LOW | synonymous_codon | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0319757143 | A -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |