| Variant ID: vg0402823034 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2823034 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAGTTCACACATCCTATACACATAAATTTCCTTGCACATGATTAATGCACACCAACTAAGAAATATCGTAAAAAATTCTAGAAAAAGTACAAATAATACG[G/A]
AAACTCAGGACTGCGTTTAAAATGGGATGGAGTTAGCACTTTGCTAATTAGTTGCTCCTTACCTAGCATAGTTATTGGTATTTATCTCTTTCATCAAAAG
CTTTTGATGAAAGAGATAAATACCAATAACTATGCTAGGTAAGGAGCAACTAATTAGCAAAGTGCTAACTCCATCCCATTTTAAACGCAGTCCTGAGTTT[C/T]
CGTATTATTTGTACTTTTTCTAGAATTTTTTACGATATTTCTTAGTTGGTGTGCATTAATCATGTGCAAGGAAATTTATGTGTATAGGATGTGTGAACTT
| 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 | 78.30% | 10.20% | 3.15% | 8.38% | NA |
| All Indica | 2759 | 76.10% | 11.50% | 3.66% | 8.77% | NA |
| All Japonica | 1512 | 87.80% | 9.50% | 1.26% | 1.46% | NA |
| Aus | 269 | 52.40% | 5.90% | 6.69% | 34.94% | NA |
| Indica I | 595 | 99.20% | 0.20% | 0.00% | 0.67% | NA |
| Indica II | 465 | 83.90% | 5.20% | 3.44% | 7.53% | NA |
| Indica III | 913 | 52.60% | 24.90% | 6.90% | 15.66% | NA |
| Indica Intermediate | 786 | 81.40% | 8.10% | 2.80% | 7.63% | NA |
| Temperate Japonica | 767 | 81.90% | 17.60% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 93.10% | 0.40% | 2.78% | 3.77% | NA |
| Japonica Intermediate | 241 | 95.40% | 2.90% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 58.30% | 2.10% | 5.21% | 34.38% | NA |
| Intermediate | 90 | 83.30% | 4.40% | 6.67% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402823034 | G -> DEL | N | N | silent_mutation | Average:46.22; most accessible tissue: Callus, score: 67.896 | N | N | N | N |
| vg0402823034 | G -> A | LOC_Os04g05570.1 | upstream_gene_variant ; 1141.0bp to feature; MODIFIER | silent_mutation | Average:46.22; most accessible tissue: Callus, score: 67.896 | N | N | N | N |
| vg0402823034 | G -> A | LOC_Os04g05580.1 | upstream_gene_variant ; 3116.0bp to feature; MODIFIER | silent_mutation | Average:46.22; most accessible tissue: Callus, score: 67.896 | N | N | N | N |
| vg0402823034 | G -> A | LOC_Os04g05570-LOC_Os04g05580 | intergenic_region ; MODIFIER | silent_mutation | Average:46.22; most accessible tissue: Callus, score: 67.896 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402823034 | NA | 2.62E-09 | Awn_length | Jap_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 |
| vg0402823034 | 4.52E-06 | NA | Heading_date | 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 |
| vg0402823034 | NA | 7.11E-06 | mr1549_2 | 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 |
| vg0402823034 | 1.81E-06 | 6.56E-11 | mr1798_2 | 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 |