| Variant ID: vg0319757071 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757071 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )
CTTGGTGAATGCTACTGACATTGCACGCTTTATTCGAGTGGTCGCTAATGAGGCAAGAACCATGGTTGTTGGTGGTATCATCATCATTAGTATTGCTAGT[G/A]
TTGTTGTCTGCATTGCGTCCATCTTCTTGGGGCAGGAACTCTTGATGCACAACAGAAGATCCGGTGATCTGAAGTGGCTCAGTGCGCTGTCTTTGGTTAC
GTAACCAAAGACAGCGCACTGAGCCACTTCAGATCACCGGATCTTCTGTTGTGCATCAAGAGTTCCTGCCCCAAGAAGATGGACGCAATGCAGACAACAA[C/T]
ACTAGCAATACTAATGATGATGATACCACCAACAACCATGGTTCTTGCCTCATTAGCGACCACTCGAATAAAGCGTGCAATGTCAGTAGCATTCACCAAG
| 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 | 31.80% | 0.20% | 4.46% | 63.52% | NA |
| All Indica | 2759 | 4.10% | 0.00% | 4.64% | 91.30% | NA |
| All Japonica | 1512 | 81.50% | 0.60% | 5.16% | 12.76% | NA |
| Aus | 269 | 13.00% | 0.00% | 0.74% | 86.25% | NA |
| Indica I | 595 | 3.20% | 0.00% | 2.02% | 94.79% | NA |
| Indica II | 465 | 4.70% | 0.00% | 2.15% | 93.12% | NA |
| Indica III | 913 | 2.80% | 0.00% | 7.78% | 89.38% | NA |
| Indica Intermediate | 786 | 5.70% | 0.00% | 4.45% | 89.82% | NA |
| Temperate Japonica | 767 | 90.50% | 1.20% | 2.87% | 5.48% | NA |
| Tropical Japonica | 504 | 66.10% | 0.00% | 7.94% | 25.99% | NA |
| Japonica Intermediate | 241 | 85.10% | 0.00% | 6.64% | 8.30% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 0.00% | 19.79% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 3.33% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757071 | G -> A | LOC_Os03g35670.1 | synonymous_variant ; p.Asn651Asn; LOW | synonymous_codon | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0319757071 | G -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |