| Variant ID: vg1114173769 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14173769 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 309. )
GCGTTCTGAAGAAGTATGTTCGTAACCGTGCTCGTCCAGAGGCAAGCATCGCCAAGGGTTATGGAACAGAGGAGGTCATCGAATTTTGCGTAGAATTTAT[C/T]
GAAGACCTTCGCCCAATCGGGGTACCTGAATCACGCCATGAAGGGAGACTACGGGGAAAGGGAACTCTCGGAAGGAAAGCAATAACGACGGTAGACAACA
TGTTGTCTACCGTCGTTATTGCTTTCCTTCCGAGAGTTCCCTTTCCCCGTAGTCTCCCTTCATGGCGTGATTCAGGTACCCCGATTGGGCGAAGGTCTTC[G/A]
ATAAATTCTACGCAAAATTCGATGACCTCCTCTGTTCCATAACCCTTGGCGATGCTTGCCTCTGGACGAGCACGGTTACGAACATACTTCTTCAGAACGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.20% | 1.10% | 3.85% | 59.84% | NA |
| All Indica | 2759 | 3.20% | 1.30% | 5.18% | 90.32% | NA |
| All Japonica | 1512 | 96.50% | 0.10% | 0.53% | 2.91% | NA |
| Aus | 269 | 1.50% | 3.70% | 8.55% | 86.25% | NA |
| Indica I | 595 | 3.20% | 0.80% | 2.35% | 93.61% | NA |
| Indica II | 465 | 0.90% | 1.70% | 6.24% | 91.18% | NA |
| Indica III | 913 | 2.00% | 1.30% | 6.68% | 90.03% | NA |
| Indica Intermediate | 786 | 6.00% | 1.40% | 4.96% | 87.66% | NA |
| Temperate Japonica | 767 | 96.30% | 0.00% | 0.26% | 3.39% | NA |
| Tropical Japonica | 504 | 96.20% | 0.20% | 0.79% | 2.78% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.83% | 1.66% | NA |
| VI/Aromatic | 96 | 83.30% | 3.10% | 4.17% | 9.38% | NA |
| Intermediate | 90 | 37.80% | 1.10% | 4.44% | 56.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114173769 | C -> T | LOC_Os11g24860.1 | synonymous_variant ; p.Ile800Ile; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1114173769 | C -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |