| Variant ID: vg0317761884 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17761884 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAGGCATCATGTAGAACAGGAACAAGAACAGGAACAAGAATATAGCGCACATAGTATAGCGCTAACAATGGGAACAGGAATAGCGCTAACAGCAGTAGCA[G/A]
GAGGAGAAGATTATACCCCGAGAATGGCCCTCCGCTGGATGGTGAGGCAGAATTGCCTCCGTTGTTGTAGTCGTTCACGGCACCTCCTCCTGGCGCACCA
TGGTGCGCCAGGAGGAGGTGCCGTGAACGACTACAACAACGGAGGCAATTCTGCCTCACCATCCAGCGGAGGGCCATTCTCGGGGTATAATCTTCTCCTC[C/T]
TGCTACTGCTGTTAGCGCTATTCCTGTTCCCATTGTTAGCGCTATACTATGTGCGCTATATTCTTGTTCCTGTTCTTGTTCCTGTTCTACATGATGCCTC
| 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% | 4.04% | 64.30% | NA |
| All Indica | 2759 | 3.30% | 0.00% | 4.82% | 91.92% | NA |
| All Japonica | 1512 | 83.50% | 0.50% | 1.39% | 14.62% | NA |
| Aus | 269 | 3.00% | 0.00% | 10.78% | 86.25% | NA |
| Indica I | 595 | 3.90% | 0.00% | 13.11% | 83.03% | NA |
| Indica II | 465 | 3.70% | 0.00% | 1.72% | 94.62% | NA |
| Indica III | 913 | 2.30% | 0.00% | 2.30% | 95.40% | NA |
| Indica Intermediate | 786 | 3.70% | 0.00% | 3.31% | 93.00% | NA |
| Temperate Japonica | 767 | 96.60% | 0.90% | 2.22% | 0.26% | NA |
| Tropical Japonica | 504 | 63.30% | 0.00% | 0.60% | 36.11% | NA |
| Japonica Intermediate | 241 | 84.20% | 0.00% | 0.41% | 15.35% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 4.17% | 9.38% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 4.44% | 45.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761884 | G -> A | LOC_Os03g31190.1 | synonymous_variant ; p.Leu62Leu; LOW | synonymous_codon | Average:5.505; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |
| vg0317761884 | G -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:5.505; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |