| Variant ID: vg0317761627 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 17761627 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 80. )
CTAAACTTGTACCGTTGTGTCATTCCGGTCCCTAAACTCGCAAATCGACCGTTTAGGTTCTCAAACTTGTTCGACTGTGTCATCCCGATCTCTAAACTGT[T/A]
GGAAATATAGTCATTAATCGGCATATTTTAATCCAAGAAAATGAAACAATGATCATGGCATAAGCAGTGTAGGGTGATCTTAACATAACCAGTAGCATAC
GTATGCTACTGGTTATGTTAAGATCACCCTACACTGCTTATGCCATGATCATTGTTTCATTTTCTTGGATTAAAATATGCCGATTAATGACTATATTTCC[A/T]
ACAGTTTAGAGATCGGGATGACACAGTCGAACAAGTTTGAGAACCTAAACGGTCGATTTGCGAGTTTAGGGACCGGAATGACACAACGGTACAAGTTTAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.90% | 0.70% | 3.75% | 61.68% | NA |
| All Indica | 2759 | 6.50% | 0.80% | 3.99% | 88.66% | NA |
| All Japonica | 1512 | 85.20% | 0.40% | 2.58% | 11.84% | NA |
| Aus | 269 | 3.30% | 1.10% | 7.81% | 87.73% | NA |
| Indica I | 595 | 5.40% | 0.30% | 3.53% | 90.76% | NA |
| Indica II | 465 | 7.30% | 1.10% | 2.37% | 89.25% | NA |
| Indica III | 913 | 6.00% | 1.00% | 4.05% | 88.94% | NA |
| Indica Intermediate | 786 | 7.50% | 0.90% | 5.22% | 86.39% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 63.70% | 0.60% | 3.37% | 32.34% | NA |
| Japonica Intermediate | 241 | 83.80% | 1.20% | 9.13% | 5.81% | NA |
| VI/Aromatic | 96 | 84.40% | 1.00% | 3.12% | 11.46% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 4.44% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0317761627 | T -> A | LOC_Os03g31190.1 | synonymous_variant ; p.Pro147Pro; LOW | synonymous_codon | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0317761627 | T -> DEL | LOC_Os03g31190.1 | N | frameshift_variant | Average:34.876; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |