| Variant ID: vg0826584838 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 26584838 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 123. )
AAAGCCACTAGTGGATATGTTTTCACACTGGGTGGTGGTGCTGTTTCATGGAGGTCTTGCAAACAGACAATTTTGACGAGGTCAACCATGGAAGCAGAGC[T/C]
AACGGCACTGGATACTGCTACTGTTGAGGCAGAATGGCTGCGTGATCTATTAATGGATCTGCCTGTTGTTGAAAAACCGGTGCCGGCTATCCTTATGAAC
GTTCATAAGGATAGCCGGCACCGGTTTTTCAACAACAGGCAGATCCATTAATAGATCACGCAGCCATTCTGCCTCAACAGTAGCAGTATCCAGTGCCGTT[A/G]
GCTCTGCTTCCATGGTTGACCTCGTCAAAATTGTCTGTTTGCAAGACCTCCATGAAACAGCACCACCACCCAGTGTGAAAACATATCCACTAGTGGCTTT
| 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 | 2.60% | 0.60% | 27.93% | 68.96% | NA |
| All Indica | 2759 | 0.10% | 0.80% | 23.49% | 75.64% | NA |
| All Japonica | 1512 | 4.40% | 0.10% | 35.71% | 59.79% | NA |
| Aus | 269 | 0.70% | 0.00% | 25.28% | 73.98% | NA |
| Indica I | 595 | 0.00% | 0.00% | 17.48% | 82.52% | NA |
| Indica II | 465 | 0.00% | 1.10% | 5.59% | 93.33% | NA |
| Indica III | 913 | 0.10% | 1.00% | 37.57% | 61.34% | NA |
| Indica Intermediate | 786 | 0.10% | 1.00% | 22.26% | 76.59% | NA |
| Temperate Japonica | 767 | 2.50% | 0.10% | 32.20% | 65.19% | NA |
| Tropical Japonica | 504 | 7.70% | 0.00% | 43.45% | 48.81% | NA |
| Japonica Intermediate | 241 | 3.70% | 0.00% | 30.71% | 65.56% | NA |
| VI/Aromatic | 96 | 47.90% | 0.00% | 37.50% | 14.58% | NA |
| Intermediate | 90 | 4.40% | 3.30% | 31.11% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0826584838 | T -> C | LOC_Os08g42090.1 | missense_variant ; p.Leu1194Pro; MODERATE | nonsynonymous_codon ; L1194P | Average:9.425; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0826584838 | T -> DEL | LOC_Os08g42090.1 | N | frameshift_variant | Average:9.425; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |