| Variant ID: vg0722555376 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 22555376 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTGCATCCTTTTGCAATGTCATGTGGGATGGGTCCTAATACTCAGCTATATATTGTTTACCATATGCCGTTGATAACTTGGGTATCAAAATGACTAGAT[G/A]
TTGGTTTAGGAAATGCTTAGCCATGCTTAGTTCAACTAGCACACACACGGGGATCACATTATTACATAGACTTTGACTATGAGCATAGCTTTGGTTTGGT
ACCAAACCAAAGCTATGCTCATAGTCAAAGTCTATGTAATAATGTGATCCCCGTGTGTGTGCTAGTTGAACTAAGCATGGCTAAGCATTTCCTAAACCAA[C/T]
ATCTAGTCATTTTGATACCCAAGTTATCAACGGCATATGGTAAACAATATATAGCTGAGTATTAGGACCCATCCCACATGACATTGCAAAAGGATGCAAC
| 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 | 88.50% | 2.10% | 6.62% | 2.71% | NA |
| All Indica | 2759 | 85.60% | 3.70% | 9.79% | 0.94% | NA |
| All Japonica | 1512 | 91.00% | 0.00% | 2.51% | 6.48% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 65.90% | 6.60% | 27.39% | 0.17% | NA |
| Indica II | 465 | 87.50% | 5.60% | 6.45% | 0.43% | NA |
| Indica III | 913 | 96.30% | 1.80% | 1.64% | 0.33% | NA |
| Indica Intermediate | 786 | 87.00% | 2.50% | 7.89% | 2.54% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.26% | 1.30% | NA |
| Tropical Japonica | 504 | 78.20% | 0.00% | 5.95% | 15.87% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 2.49% | 3.32% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 4.44% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0722555376 | G -> DEL | N | N | silent_mutation | Average:9.591; most accessible tissue: Callus, score: 16.625 | N | N | N | N |
| vg0722555376 | G -> A | LOC_Os07g37620-LOC_Os07g37630 | intergenic_region ; MODIFIER | silent_mutation | Average:9.591; most accessible tissue: Callus, score: 16.625 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0722555376 | 6.28E-06 | NA | mr1594_2 | 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 |
| vg0722555376 | 4.99E-06 | 2.51E-07 | mr1835_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 |