| Variant ID: vg0300825597 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 825597 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AATGCGTCACCGGTTGCATGGCCGCCCTAAGTCGGTTCATATCGAGGCTGGGAGAGAAGGCGTTACCCTTATTTAAGCTTCTCAAACGCTCCGGACCGTT[T/C]
ACCTGGACGGAGGAAGCCGAAAATGCCCTCACTCAGTTGAAGGCATGTCTAAGCTCTCCCCCAGTTCTGGTCGCCCCGGAGCCAGACGAGCCCTTGTTAC
GTAACAAGGGCTCGTCTGGCTCCGGGGCGACCAGAACTGGGGGAGAGCTTAGACATGCCTTCAACTGAGTGAGGGCATTTTCGGCTTCCTCCGTCCAGGT[A/G]
AACGGTCCGGAGCGTTTGAGAAGCTTAAATAAGGGTAACGCCTTCTCTCCCAGCCTCGATATGAACCGACTTAGGGCGGCCATGCAACCGGTGACGCATT
| 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 | 17.80% | 0.80% | 2.81% | 78.59% | NA |
| All Indica | 2759 | 7.80% | 1.30% | 3.77% | 87.13% | NA |
| All Japonica | 1512 | 37.90% | 0.00% | 1.32% | 60.78% | NA |
| Aus | 269 | 4.50% | 0.00% | 0.74% | 94.80% | NA |
| Indica I | 595 | 8.60% | 1.20% | 2.18% | 88.07% | NA |
| Indica II | 465 | 8.80% | 2.40% | 5.16% | 83.66% | NA |
| Indica III | 913 | 6.90% | 0.90% | 3.07% | 89.16% | NA |
| Indica Intermediate | 786 | 7.60% | 1.30% | 4.96% | 86.13% | NA |
| Temperate Japonica | 767 | 61.30% | 0.00% | 0.39% | 38.33% | NA |
| Tropical Japonica | 504 | 7.10% | 0.00% | 1.98% | 90.87% | NA |
| Japonica Intermediate | 241 | 27.80% | 0.00% | 2.90% | 69.29% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 1.04% | 73.96% | NA |
| Intermediate | 90 | 20.00% | 1.10% | 6.67% | 72.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300825597 | T -> C | LOC_Os03g02350.1 | synonymous_variant ; p.Phe1092Phe; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0300825597 | T -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |