| Variant ID: vg0512046891 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12046891 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGCATTTGCAAAAGCAGCATTTAGCAGACATTTGAGAATTTGATAAAACAGTTAAGTAATTAAACAATATTAATCCAACGCTATACAACATACCCTGTTG[T/C]
ATAGGCCCAACCATTCTGAACAACCACCCCGGCTGCAAAGTTCTATCTCCAAACCAGGAATGTACCATTCCAAACCAGGAGCTAATCAAATTATTACCAG
CTGGTAATAATTTGATTAGCTCCTGGTTTGGAATGGTACATTCCTGGTTTGGAGATAGAACTTTGCAGCCGGGGTGGTTGTTCAGAATGGTTGGGCCTAT[A/G]
CAACAGGGTATGTTGTATAGCGTTGGATTAATATTGTTTAATTACTTAACTGTTTTATCAAATTCTCAAATGTCTGCTAAATGCTGCTTTTGCAAATGCA
| 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 | 84.10% | 0.10% | 6.12% | 9.67% | NA |
| All Indica | 2759 | 84.20% | 0.20% | 7.29% | 8.37% | NA |
| All Japonica | 1512 | 94.20% | 0.00% | 5.36% | 0.40% | NA |
| Aus | 269 | 21.20% | 0.00% | 0.74% | 78.07% | NA |
| Indica I | 595 | 87.60% | 0.20% | 7.73% | 4.54% | NA |
| Indica II | 465 | 94.80% | 0.20% | 3.87% | 1.08% | NA |
| Indica III | 913 | 76.20% | 0.10% | 9.64% | 14.02% | NA |
| Indica Intermediate | 786 | 84.50% | 0.30% | 6.23% | 9.03% | NA |
| Temperate Japonica | 767 | 89.70% | 0.00% | 10.17% | 0.13% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 1.24% | 0.41% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 3.33% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512046891 | T -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:37.37; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0512046891 | T -> C | LOC_Os05g20520.1 | missense_variant ; p.Tyr24Cys; MODERATE | nonsynonymous_codon ; Y24C | Average:37.37; most accessible tissue: Zhenshan97 panicle, score: 68.538 | unknown | unknown | TOLERATED | 0.24 |