| Variant ID: vg0431509763 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 31509763 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, C: 0.10, others allele: 0.00, population size: 241. )
GAAAAAAAATAGTAAGGTGACTATGAGTACTAACAAAAGAGTCGTTGAACAAGAAAAGCAGAGAACTATCTCAAGCCAGCATTGGACTGTGACCAAAATT[G/C]
TAAAAACCATTGTACTAATTTTCTCTGCCAAAGACAGATGAAAATTAACTGGTACAAGAATGATTATCAATCCAAACATATAAGTTCAGAAAATGATATA
TATATCATTTTCTGAACTTATATGTTTGGATTGATAATCATTCTTGTACCAGTTAATTTTCATCTGTCTTTGGCAGAGAAAATTAGTACAATGGTTTTTA[C/G]
AATTTTGGTCACAGTCCAATGCTGGCTTGAGATAGTTCTCTGCTTTTCTTGTTCAACGACTCTTTTGTTAGTACTCATAGTCACCTTACTATTTTTTTTC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.60% | 24.40% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 73.20% | 26.70% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 76.90% | 23.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 87.70% | 12.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 52.90% | 46.70% | 0.34% | 0.00% | NA |
| Indica II | 465 | 73.10% | 26.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 85.00% | 15.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 74.90% | 24.90% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 42.90% | 57.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 87.10% | 12.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 82.30% | 17.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 17.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0431509763 | G -> C | LOC_Os04g52900.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.015; most accessible tissue: Zhenshan97 root, score: 80.208 | N | N | N | N |
| vg0431509763 | G -> C | LOC_Os04g52900.2 | intron_variant ; MODIFIER | silent_mutation | Average:49.015; most accessible tissue: Zhenshan97 root, score: 80.208 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0431509763 | NA | 4.81E-12 | Spikelet_length | Ind_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 |
| vg0431509763 | NA | 4.29E-07 | mr1271 | 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 |