| Variant ID: vg0319757925 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757925 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATGTTGGTTTGGTTAACCACAATTTGGATTAGCTCTGGTGAGGTTTCGTTGATGCTTTTCTCATTCCCATTGGCTTGGGTTCTTTATCTTGTACTTGATT[T/C]
CTTGGCTGCTGTGCTCGAACATCCAAAGGTACAATGCCGATACTGGCCTCGGTCTTGTCAACTGATGGCTGGGGCTGAAATTGGGCATTGACACCTTGTG
CACAAGGTGTCAATGCCCAATTTCAGCCCCAGCCATCAGTTGACAAGACCGAGGCCAGTATCGGCATTGTACCTTTGGATGTTCGAGCACAGCAGCCAAG[A/G]
AATCAAGTACAAGATAAAGAACCCAAGCCAATGGGAATGAGAAAAGCATCAACGAAACCTCACCAGAGCTAATCCAAATTGTGGTTAACCAAACCAACAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.20% | 0.40% | 5.35% | 62.04% | NA |
| All Indica | 2759 | 3.90% | 0.60% | 7.03% | 88.44% | NA |
| All Japonica | 1512 | 84.00% | 0.00% | 3.24% | 12.76% | NA |
| Aus | 269 | 10.00% | 0.00% | 1.49% | 88.48% | NA |
| Indica I | 595 | 3.70% | 0.00% | 4.37% | 91.93% | NA |
| Indica II | 465 | 4.50% | 0.00% | 5.38% | 90.11% | NA |
| Indica III | 913 | 3.10% | 1.50% | 10.41% | 84.99% | NA |
| Indica Intermediate | 786 | 4.70% | 0.40% | 6.11% | 88.80% | NA |
| Temperate Japonica | 767 | 94.90% | 0.00% | 0.52% | 4.56% | NA |
| Tropical Japonica | 504 | 66.70% | 0.00% | 6.75% | 26.59% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 4.56% | 9.96% | NA |
| VI/Aromatic | 96 | 74.00% | 0.00% | 0.00% | 26.04% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 6.67% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757925 | T -> C | LOC_Os03g35670.1 | synonymous_variant ; p.Arg407Arg; LOW | synonymous_codon | Average:5.394; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |
| vg0319757925 | T -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:5.394; most accessible tissue: Minghui63 flower, score: 7.958 | N | N | N | N |