| Variant ID: vg0319756963 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19756963 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 254. )
CATTGGCATCAGTGGTACCATAGTTGCTATCACCATTGGAGTCTTTCTCAGTGTCAAAATTGCTAAGGTTGTCATTCTGGATTCCAACATTGATACTATC[G/A]
TTGACATCTTGGTGAATGCTACTGACATTGCACGCTTTATTCGAGTGGTCGCTAATGAGGCAAGAACCATGGTTGTTGGTGGTATCATCATCATTAGTAT
ATACTAATGATGATGATACCACCAACAACCATGGTTCTTGCCTCATTAGCGACCACTCGAATAAAGCGTGCAATGTCAGTAGCATTCACCAAGATGTCAA[C/T]
GATAGTATCAATGTTGGAATCCAGAATGACAACCTTAGCAATTTTGACACTGAGAAAGACTCCAATGGTGATAGCAACTATGGTACCACTGATGCCAATG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.70% | 0.10% | 3.62% | 66.61% | NA |
| All Indica | 2759 | 2.40% | 0.00% | 1.99% | 95.54% | NA |
| All Japonica | 1512 | 78.90% | 0.30% | 6.75% | 14.09% | NA |
| Aus | 269 | 10.00% | 0.00% | 2.23% | 87.73% | NA |
| Indica I | 595 | 2.40% | 0.00% | 0.17% | 97.48% | NA |
| Indica II | 465 | 3.40% | 0.00% | 0.22% | 96.34% | NA |
| Indica III | 913 | 1.30% | 0.00% | 3.94% | 94.74% | NA |
| Indica Intermediate | 786 | 3.20% | 0.10% | 2.16% | 94.53% | NA |
| Temperate Japonica | 767 | 91.90% | 0.00% | 2.09% | 6.00% | NA |
| Tropical Japonica | 504 | 58.70% | 0.80% | 12.30% | 28.17% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.00% | 9.96% | 10.37% | NA |
| VI/Aromatic | 96 | 74.00% | 0.00% | 5.21% | 20.83% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 3.33% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319756963 | G -> A | LOC_Os03g35670.1 | synonymous_variant ; p.Asn687Asn; LOW | synonymous_codon | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0319756963 | G -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |