| Variant ID: vg0420968069 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20968069 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGTGCTTTCCATGGTTTTAGATAATATGCCAGGCTAGCAAAATGCTCCATCGATTCTATGCGATCTCTCTTCAAGAAAGAAGTTATGATTGAAAATTCAT[A/C]
ACATTGATATATATCTGCACTTTTGTAGTTTGAAGAGGGAGTGACCCCCAGTGCATATGCCTTTGCCTTAGTGGAACAGCGGGGTGGCAGAGAAACGATT
AATCGTTTCTCTGCCACCCCGCTGTTCCACTAAGGCAAAGGCATATGCACTGGGGGTCACTCCCTCTTCAAACTACAAAAGTGCAGATATATATCAATGT[T/G]
ATGAATTTTCAATCATAACTTCTTTCTTGAAGAGAGATCGCATAGAATCGATGGAGCATTTTGCTAGCCTGGCATATTATCTAAAACCATGGAAAGCACT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.10% | 0.30% | 13.03% | 30.60% | NA |
| All Indica | 2759 | 39.00% | 0.40% | 10.62% | 49.91% | NA |
| All Japonica | 1512 | 91.80% | 0.00% | 5.49% | 2.71% | NA |
| Aus | 269 | 26.80% | 0.00% | 69.14% | 4.09% | NA |
| Indica I | 595 | 78.00% | 0.20% | 0.84% | 21.01% | NA |
| Indica II | 465 | 16.80% | 0.90% | 7.96% | 74.41% | NA |
| Indica III | 913 | 31.70% | 0.30% | 17.20% | 50.82% | NA |
| Indica Intermediate | 786 | 31.30% | 0.50% | 11.96% | 56.23% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 79.20% | 0.00% | 14.09% | 6.75% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 4.98% | 2.49% | NA |
| VI/Aromatic | 96 | 55.20% | 0.00% | 41.67% | 3.12% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 15.56% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420968069 | A -> C | LOC_Os04g34650.1 | upstream_gene_variant ; 3401.0bp to feature; MODIFIER | silent_mutation | Average:17.193; most accessible tissue: Zhenshan97 flower, score: 34.767 | N | N | N | N |
| vg0420968069 | A -> C | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.193; most accessible tissue: Zhenshan97 flower, score: 34.767 | N | N | N | N |
| vg0420968069 | A -> DEL | N | N | silent_mutation | Average:17.193; most accessible tissue: Zhenshan97 flower, score: 34.767 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0420968069 | NA | 6.59E-10 | Heading_date | Ind_All | Not | 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 |
| vg0420968069 | NA | 3.93E-06 | mr1075 | 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 |