| Variant ID: vg0319757074 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757074 |
| 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. )
GGTGAATGCTACTGACATTGCACGCTTTATTCGAGTGGTCGCTAATGAGGCAAGAACCATGGTTGTTGGTGGTATCATCATCATTAGTATTGCTAGTGTT[G/A]
TTGTCTGCATTGCGTCCATCTTCTTGGGGCAGGAACTCTTGATGCACAACAGAAGATCCGGTGATCTGAAGTGGCTCAGTGCGCTGTCTTTGGTTACCAC
GTGGTAACCAAAGACAGCGCACTGAGCCACTTCAGATCACCGGATCTTCTGTTGTGCATCAAGAGTTCCTGCCCCAAGAAGATGGACGCAATGCAGACAA[C/T]
AACACTAGCAATACTAATGATGATGATACCACCAACAACCATGGTTCTTGCCTCATTAGCGACCACTCGAATAAAGCGTGCAATGTCAGTAGCATTCACC
| 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 | 31.50% | 0.10% | 2.35% | 66.04% | NA |
| All Indica | 2759 | 2.90% | 0.20% | 2.54% | 94.35% | NA |
| All Japonica | 1512 | 83.50% | 0.00% | 1.98% | 14.55% | NA |
| Aus | 269 | 10.40% | 0.00% | 1.12% | 88.48% | NA |
| Indica I | 595 | 1.70% | 0.20% | 0.50% | 97.65% | NA |
| Indica II | 465 | 3.90% | 0.00% | 1.08% | 95.05% | NA |
| Indica III | 913 | 2.20% | 0.20% | 4.05% | 93.54% | NA |
| Indica Intermediate | 786 | 4.10% | 0.40% | 3.18% | 92.37% | NA |
| Temperate Japonica | 767 | 94.70% | 0.00% | 0.91% | 4.43% | NA |
| Tropical Japonica | 504 | 65.50% | 0.00% | 2.58% | 31.94% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 4.15% | 10.37% | NA |
| VI/Aromatic | 96 | 75.00% | 0.00% | 4.17% | 20.83% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 4.44% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757074 | G -> A | LOC_Os03g35670.1 | synonymous_variant ; p.Asn650Asn; LOW | synonymous_codon | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0319757074 | G -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |