| Variant ID: vg0811251746 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11251746 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )
AAAGGTCATAGGTTCTTCTCCGTTTGACCTCTTTTGCGGCATTTCTTCTTTCAGCATATGATTTTCTTATGCTAAAGCCTTTATCCCAAGCGTACTTGTT[G/T,A]
TAGAAGTGAATTCCTTCATCCTCACTATTGAATGTCTTGCTGACAATTTGTTGGTACTCCAACAATTCCTCAACCGATATCCCTGTATCCTCCATCAGTG
CACTGATGGAGGATACAGGGATATCGGTTGAGGAATTGTTGGAGTACCAACAAATTGTCAGCAAGACATTCAATAGTGAGGATGAAGGAATTCACTTCTA[C/A,T]
AACAAGTACGCTTGGGATAAAGGCTTTAGCATAAGAAAATCATATGCTGAAAGAAGAAATGCCGCAAAAGAGGTCAAACGGAGAAGAACCTATGACCTTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.00% | 1.90% | 0.00% | 0.00% | A: 0.04% |
| All Indica | 2759 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 90.90% | 9.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 0.00% | A: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811251746 | G -> T | LOC_Os08g18850.1 | stop_gained ; p.Tyr32*; HIGH | stop_gained | Average:13.727; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
| vg0811251746 | G -> A | LOC_Os08g18850.1 | synonymous_variant ; p.Tyr32Tyr; LOW | synonymous_codon | Average:13.727; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |