| Variant ID: vg0319757767 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757767 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CACTGGCTTCCATAGGATCGACGGCAATGGCAAAGGTTGGAGGCTCAGTTTTGAGAAATTCTGATAACTTGCACTGTTGCTGGACTGTAGGTACTTGAAC[G/A]
TTGGTTGTCCCTGCTGGGTTGTTCCAATTCTGTAATAGTTGAAAGGCTGTTGCCAACATGTTGGTTTGGTTAACCACAATTTGGATTAGCTCTGGTGAGG
CCTCACCAGAGCTAATCCAAATTGTGGTTAACCAAACCAACATGTTGGCAACAGCCTTTCAACTATTACAGAATTGGAACAACCCAGCAGGGACAACCAA[C/T]
GTTCAAGTACCTACAGTCCAGCAACAGTGCAAGTTATCAGAATTTCTCAAAACTGAGCCTCCAACCTTTGCCATTGCCGTCGATCCTATGGAAGCCAGTG
| 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 | 31.30% | 0.40% | 16.21% | 52.03% | NA |
| All Indica | 2759 | 3.10% | 0.00% | 23.96% | 72.92% | NA |
| All Japonica | 1512 | 82.30% | 1.20% | 3.04% | 13.43% | NA |
| Aus | 269 | 11.90% | 0.00% | 12.27% | 75.84% | NA |
| Indica I | 595 | 3.50% | 0.00% | 14.79% | 81.68% | NA |
| Indica II | 465 | 3.90% | 0.00% | 21.08% | 75.05% | NA |
| Indica III | 913 | 1.80% | 0.00% | 32.09% | 66.16% | NA |
| Indica Intermediate | 786 | 3.80% | 0.10% | 23.16% | 72.90% | NA |
| Temperate Japonica | 767 | 94.40% | 0.00% | 0.39% | 5.22% | NA |
| Tropical Japonica | 504 | 62.50% | 3.60% | 7.14% | 26.79% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 2.90% | 11.62% | NA |
| VI/Aromatic | 96 | 75.00% | 0.00% | 7.29% | 17.71% | NA |
| Intermediate | 90 | 52.20% | 1.10% | 21.11% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757767 | G -> A | LOC_Os03g35670.1 | synonymous_variant ; p.Asn419Asn; LOW | synonymous_codon | Average:5.634; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg0319757767 | G -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:5.634; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |