| Variant ID: vg0811251629 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11251629 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, T: 0.03, others allele: 0.00, population size: 191. )
AACAACATATCAACACAAGTAGTCTGACTCATGGTGAGCATGCTCACAAACACCAATATCATACCCGCTAGATAAATATGTCAGACAAACTTCATCAACA[A/T]
TAGCCTTTTTACAACAAAAGGTCATAGGTTCTTCTCCGTTTGACCTCTTTTGCGGCATTTCTTCTTTCAGCATATGATTTTCTTATGCTAAAGCCTTTAT
ATAAAGGCTTTAGCATAAGAAAATCATATGCTGAAAGAAGAAATGCCGCAAAAGAGGTCAAACGGAGAAGAACCTATGACCTTTTGTTGTAAAAAGGCTA[T/A]
TGTTGATGAAGTTTGTCTGACATATTTATCTAGCGGGTATGATATTGGTGTTTGTGAGCATGCTCACCATGAGTCAGACTACTTGTGTTGATATGTTGTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 18.20% | 1.60% | 32.88% | 47.33% | NA |
| All Indica | 2759 | 1.90% | 2.40% | 36.14% | 59.55% | NA |
| All Japonica | 1512 | 51.70% | 0.30% | 18.06% | 29.89% | NA |
| Aus | 269 | 1.50% | 1.10% | 91.82% | 5.58% | NA |
| Indica I | 595 | 1.70% | 1.50% | 19.83% | 76.97% | NA |
| Indica II | 465 | 2.80% | 2.80% | 30.32% | 64.09% | NA |
| Indica III | 913 | 1.60% | 2.60% | 48.63% | 47.10% | NA |
| Indica Intermediate | 786 | 1.80% | 2.70% | 37.40% | 58.14% | NA |
| Temperate Japonica | 767 | 85.30% | 0.10% | 4.30% | 10.30% | NA |
| Tropical Japonica | 504 | 10.70% | 0.40% | 38.89% | 50.00% | NA |
| Japonica Intermediate | 241 | 30.70% | 0.80% | 18.26% | 50.21% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 13.54% | 85.42% | NA |
| Intermediate | 90 | 22.20% | 1.10% | 26.67% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811251629 | A -> T | LOC_Os08g18850.1 | missense_variant ; p.Ile58Asn; MODERATE | nonsynonymous_codon ; I58D | Average:14.934; most accessible tissue: Zhenshan97 panicle, score: 32.308 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0811251629 | A -> T | LOC_Os08g18850.1 | missense_variant ; p.Ile58Asn; MODERATE | nonsynonymous_codon ; I58N | Average:14.934; most accessible tissue: Zhenshan97 panicle, score: 32.308 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0811251629 | A -> DEL | LOC_Os08g18850.1 | N | frameshift_variant | Average:14.934; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |