| Variant ID: vg0141809326 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41809326 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGCTCGGAAGTCGGAGGCGCGCTTCGTCGGCGAGGGGGGTGTAGAACCAGTCGCTCTTCCAGTCATCCCACTTCTTGCGGAGGACGCAGGGAATGTAGCG[G/A]
TTCAACACCGGCCCCCGCGGTTGGAAGTAGCAGCCACCAACCACCGACGGCGGCGACACCGACTGTACGGTGAAGAACCACCGGAACAGCCGAAGGGATG
CATCCCTTCGGCTGTTCCGGTGGTTCTTCACCGTACAGTCGGTGTCGCCGCCGTCGGTGGTTGGTGGCTGCTACTTCCAACCGCGGGGGCCGGTGTTGAA[C/T]
CGCTACATTCCCTGCGTCCTCCGCAAGAAGTGGGATGACTGGAAGAGCGACTGGTTCTACACCCCCCTCGCCGACGAAGCGCGCCTCCGACTTCCGAGCC
| 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 | 17.60% | 0.30% | 1.25% | 80.79% | NA |
| All Indica | 2759 | 1.80% | 0.00% | 1.45% | 96.74% | NA |
| All Japonica | 1512 | 43.50% | 0.70% | 1.06% | 54.76% | NA |
| Aus | 269 | 34.90% | 0.00% | 0.37% | 64.68% | NA |
| Indica I | 595 | 3.20% | 0.00% | 4.03% | 92.77% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.22% | 98.71% | NA |
| Indica III | 913 | 0.20% | 0.00% | 0.88% | 98.90% | NA |
| Indica Intermediate | 786 | 3.10% | 0.00% | 0.89% | 96.06% | NA |
| Temperate Japonica | 767 | 77.30% | 0.00% | 0.26% | 22.43% | NA |
| Tropical Japonica | 504 | 3.00% | 1.80% | 2.18% | 93.06% | NA |
| Japonica Intermediate | 241 | 20.70% | 0.40% | 1.24% | 77.59% | NA |
| VI/Aromatic | 96 | 10.40% | 3.10% | 0.00% | 86.46% | NA |
| Intermediate | 90 | 23.30% | 3.30% | 2.22% | 71.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0141809326 | G -> A | LOC_Os01g72070.1 | synonymous_variant ; p.Asn82Asn; LOW | synonymous_codon | Average:4.668; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0141809326 | G -> DEL | LOC_Os01g72070.1 | N | frameshift_variant | Average:4.668; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |