| Variant ID: vg0329363053 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29363053 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, A: 0.05, others allele: 0.00, population size: 57. )
ATCACAGGCCCGCCAGGCGGTCGAGGACGGCGTCATAGCCATCTCCCAGATCTACCGGCGCCCGCCAGCTGGAGGCCTGCGCCGGGGGCTGGCTCGGAAG[A/T]
CGGAGGCGCGCTTCGTCGGCGAGGGGGGTGTAGAACCAGTCGCTCTTCCAGTCATCCCACTTCTTGCGGAGGACGCAGGGAATGTAGCGGTTCAACACCG
CGGTGTTGAACCGCTACATTCCCTGCGTCCTCCGCAAGAAGTGGGATGACTGGAAGAGCGACTGGTTCTACACCCCCCTCGCCGACGAAGCGCGCCTCCG[T/A]
CTTCCGAGCCAGCCCCCGGCGCAGGCCTCCAGCTGGCGGGCGCCGGTAGATCTGGGAGATGGCTATGACGCCGTCCTCGACCGCCTGGCGGGCCTGTGAT
| 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 | 21.60% | 0.60% | 32.16% | 45.60% | NA |
| All Indica | 2759 | 3.60% | 0.60% | 31.35% | 64.48% | NA |
| All Japonica | 1512 | 56.70% | 0.70% | 38.10% | 4.50% | NA |
| Aus | 269 | 3.30% | 0.00% | 4.46% | 92.19% | NA |
| Indica I | 595 | 3.20% | 0.70% | 20.50% | 75.63% | NA |
| Indica II | 465 | 4.30% | 0.40% | 39.14% | 56.13% | NA |
| Indica III | 913 | 2.40% | 0.70% | 31.87% | 65.06% | NA |
| Indica Intermediate | 786 | 4.80% | 0.50% | 34.35% | 60.31% | NA |
| Temperate Japonica | 767 | 87.20% | 0.30% | 11.60% | 0.91% | NA |
| Tropical Japonica | 504 | 11.50% | 1.20% | 77.18% | 10.12% | NA |
| Japonica Intermediate | 241 | 53.90% | 1.20% | 40.66% | 4.15% | NA |
| VI/Aromatic | 96 | 34.40% | 1.00% | 35.42% | 29.17% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 36.67% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0329363053 | A -> T | LOC_Os03g51320.1 | synonymous_variant ; p.Arg175Arg; LOW | synonymous_codon | Average:30.522; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 | N | N | N | N |
| vg0329363053 | A -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:30.522; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 | N | N | N | N |