| Variant ID: vg0817014758 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17014758 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.07, others allele: 0.00, population size: 115. )
GAATGAAGCACCAGACACCAGTTGTGTGGCAGTGGTCCAACACCTGATTAACCAGAACAAATTGCTTATAGAGATACTACAGCAGCATCGGATGCCAATT[T/C]
TGAACCCGAGTCAGATGCAACCTCAAGTGCAGTTGGAGGCAGTCCAAGCACTCACACCACAAGTCAGCGCACCGCCAACATCCCAGAAGGCCCCTCATGC
GCATGAGGGGCCTTCTGGGATGTTGGCGGTGCGCTGACTTGTGGTGTGAGTGCTTGGACTGCCTCCAACTGCACTTGAGGTTGCATCTGACTCGGGTTCA[A/G]
AATTGGCATCCGATGCTGCTGTAGTATCTCTATAAGCAATTTGTTCTGGTTAATCAGGTGTTGGACCACTGCCACACAACTGGTGTCTGGTGCTTCATTC
| 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 | 21.90% | 8.30% | 26.17% | 43.65% | NA |
| All Indica | 2759 | 3.70% | 9.60% | 33.42% | 53.28% | NA |
| All Japonica | 1512 | 57.10% | 2.50% | 8.66% | 31.68% | NA |
| Aus | 269 | 11.90% | 16.40% | 47.21% | 24.54% | NA |
| Indica I | 595 | 4.20% | 4.20% | 15.46% | 76.13% | NA |
| Indica II | 465 | 2.40% | 5.80% | 25.81% | 66.02% | NA |
| Indica III | 913 | 3.00% | 16.20% | 50.60% | 30.23% | NA |
| Indica Intermediate | 786 | 5.00% | 8.30% | 31.55% | 55.22% | NA |
| Temperate Japonica | 767 | 73.50% | 1.70% | 4.56% | 20.21% | NA |
| Tropical Japonica | 504 | 32.90% | 2.40% | 15.08% | 49.60% | NA |
| Japonica Intermediate | 241 | 55.60% | 5.40% | 8.30% | 30.71% | NA |
| VI/Aromatic | 96 | 10.40% | 44.80% | 26.04% | 18.75% | NA |
| Intermediate | 90 | 27.80% | 3.30% | 35.56% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817014758 | T -> C | LOC_Os08g27910.1 | synonymous_variant ; p.Leu56Leu; LOW | synonymous_codon | Average:5.547; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg0817014758 | T -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.547; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |