| Variant ID: vg0817014784 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17014784 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGGCAGTGGTCCAACACCTGATTAACCAGAACAAATTGCTTATAGAGATACTACAGCAGCATCGGATGCCAATTTTGAACCCGAGTCAGATGCAACCTCA[A/G]
GTGCAGTTGGAGGCAGTCCAAGCACTCACACCACAAGTCAGCGCACCGCCAACATCCCAGAAGGCCCCTCATGCCATGCCACATGTTGACCCAAAAGAAG
CTTCTTTTGGGTCAACATGTGGCATGGCATGAGGGGCCTTCTGGGATGTTGGCGGTGCGCTGACTTGTGGTGTGAGTGCTTGGACTGCCTCCAACTGCAC[T/C]
TGAGGTTGCATCTGACTCGGGTTCAAAATTGGCATCCGATGCTGCTGTAGTATCTCTATAAGCAATTTGTTCTGGTTAATCAGGTGTTGGACCACTGCCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 18.00% | 8.20% | 28.67% | 45.18% | NA |
| All Indica | 2759 | 3.10% | 8.80% | 34.29% | 53.75% | NA |
| All Japonica | 1512 | 47.30% | 3.40% | 15.34% | 33.99% | NA |
| Aus | 269 | 9.30% | 12.60% | 45.72% | 32.34% | NA |
| Indica I | 595 | 3.20% | 4.00% | 16.64% | 76.13% | NA |
| Indica II | 465 | 3.70% | 4.90% | 27.10% | 64.30% | NA |
| Indica III | 913 | 2.10% | 14.50% | 51.26% | 32.20% | NA |
| Indica Intermediate | 786 | 3.90% | 8.30% | 32.19% | 55.60% | NA |
| Temperate Japonica | 767 | 69.10% | 2.50% | 7.69% | 20.73% | NA |
| Tropical Japonica | 504 | 17.70% | 3.60% | 23.81% | 54.96% | NA |
| Japonica Intermediate | 241 | 39.80% | 5.80% | 21.99% | 32.37% | NA |
| VI/Aromatic | 96 | 3.10% | 53.10% | 25.00% | 18.75% | NA |
| Intermediate | 90 | 22.20% | 7.80% | 33.33% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817014784 | A -> G | LOC_Os08g27910.1 | synonymous_variant ; p.Gln64Gln; LOW | synonymous_codon | Average:4.677; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0817014784 | A -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:4.677; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |