| Variant ID: vg0715506970 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 15506970 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 38. )
CTGGATCGATTATATTGGCTCAGTCTCATCATATCTATCTATCTATCTATCTATCTATTATATACTATAAGTCCATTAAACTTCCTACAAACGCTCTCAA[G/A]
CCGCCACGTGGCGCTCCTACAAATATTCCTAGGCCGCCATGTGGTATAATATAATCTCACCGTCGATTTTCAATTAAATTGGTGGACCCATTATTTTATA
TATAAAATAATGGGTCCACCAATTTAATTGAAAATCGACGGTGAGATTATATTATACCACATGGCGGCCTAGGAATATTTGTAGGAGCGCCACGTGGCGG[C/T]
TTGAGAGCGTTTGTAGGAAGTTTAATGGACTTATAGTATATAATAGATAGATAGATAGATAGATAGATATGATGAGACTGAGCCAATATAATCGATCCAG
| 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 | 77.80% | 6.80% | 9.50% | 5.88% | NA |
| All Indica | 2759 | 74.80% | 8.20% | 10.58% | 6.42% | NA |
| All Japonica | 1512 | 93.50% | 0.10% | 2.05% | 4.37% | NA |
| Aus | 269 | 22.30% | 33.50% | 41.26% | 2.97% | NA |
| Indica I | 595 | 79.70% | 6.10% | 10.76% | 3.53% | NA |
| Indica II | 465 | 68.60% | 3.90% | 8.82% | 18.71% | NA |
| Indica III | 913 | 78.00% | 10.60% | 8.21% | 3.18% | NA |
| Indica Intermediate | 786 | 71.00% | 9.70% | 14.25% | 5.09% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 1.83% | 2.35% | NA |
| Tropical Japonica | 504 | 89.10% | 0.00% | 2.78% | 8.13% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.80% | 1.24% | 2.90% | NA |
| VI/Aromatic | 96 | 75.00% | 0.00% | 6.25% | 18.75% | NA |
| Intermediate | 90 | 76.70% | 3.30% | 10.00% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715506970 | G -> DEL | N | N | silent_mutation | Average:20.383; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| vg0715506970 | G -> A | LOC_Os07g26810-LOC_Os07g26820 | intergenic_region ; MODIFIER | silent_mutation | Average:20.383; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715506970 | NA | 6.09E-06 | mr1081 | Ind_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 |
| vg0715506970 | 8.71E-06 | 8.71E-06 | mr1105 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |