| Variant ID: vg0316495531 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 16495531 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 295. )
TCCATCACGAAAGCAGCCCCTGTCAACCTTCCTCCTTTATATGTATTTAACAGAGCCCTTGCCTTATTTTCTTTTCTTTCGCACATGTCCAAAAGTTGTC[G/A]
TACTGCTGCTTTGCCTCGGCCACCATGCCCACATTGTGCATGTGCGTGCACCACTGTTAATCTCTCTCTTTAGATGACATATGAACCATACCAGTTGGTA
TACCAACTGGTATGGTTCATATGTCATCTAAAGAGAGAGATTAACAGTGGTGCACGCACATGCACAATGTGGGCATGGTGGCCGAGGCAAAGCAGCAGTA[C/T]
GACAACTTTTGGACATGTGCGAAAGAAAAGAAAATAAGGCAAGGGCTCTGTTAAATACATATAAAGGAGGAAGGTTGACAGGGGCTGCTTTCGTGATGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.70% | 5.30% | 1.18% | 11.76% | NA |
| All Indica | 2759 | 91.00% | 4.20% | 0.43% | 4.28% | NA |
| All Japonica | 1512 | 64.60% | 8.30% | 2.78% | 24.34% | NA |
| Aus | 269 | 78.80% | 0.00% | 0.74% | 20.45% | NA |
| Indica I | 595 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.80% | 1.30% | 0.00% | 1.94% | NA |
| Indica III | 913 | 87.30% | 6.10% | 0.88% | 5.70% | NA |
| Indica Intermediate | 786 | 87.00% | 5.20% | 0.51% | 7.25% | NA |
| Temperate Japonica | 767 | 54.50% | 3.30% | 4.30% | 37.94% | NA |
| Tropical Japonica | 504 | 79.60% | 11.90% | 0.60% | 7.94% | NA |
| Japonica Intermediate | 241 | 65.10% | 17.00% | 2.49% | 15.35% | NA |
| VI/Aromatic | 96 | 93.80% | 2.10% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 81.10% | 6.70% | 0.00% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0316495531 | G -> A | LOC_Os03g29035.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.761; most accessible tissue: Zhenshan97 flower, score: 86.118 | N | N | N | N |
| vg0316495531 | G -> DEL | N | N | silent_mutation | Average:61.761; most accessible tissue: Zhenshan97 flower, score: 86.118 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0316495531 | 1.36E-08 | NA | Grain_length | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0316495531 | NA | 3.87E-07 | mr1951 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |