| Variant ID: vg0722028662 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 22028662 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCATATTGGATTTATCACTACTTTGGGAAATCACCGATCTCTTACCTTTTACTTCTTTAGGTCTCCACACTCGCTTAGGTGTCGTTCGAGGCTCTAAATT[A/G]
TTACATGTTTTGTTCTCCACATCTTCGGCCTCCTTTTCTTTTTGACCTATGGCCCGAAGACGCTGAAGCCTCCTCTTTTGAGAGCGAGATAAGCCGGAAG
CTTCCGGCTTATCTCGCTCTCAAAAGAGGAGGCTTCAGCGTCTTCGGGCCATAGGTCAAAAAGAAAAGGAGGCCGAAGATGTGGAGAACAAAACATGTAA[T/C]
AATTTAGAGCCTCGAACGACACCTAAGCGAGTGTGGAGACCTAAAGAAGTAAAAGGTAAGAGATCGGTGATTTCCCAAAGTAGTGATAAATCCAATATGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.20% | 1.30% | 1.31% | 6.22% | NA |
| All Indica | 2759 | 96.40% | 0.00% | 0.22% | 3.30% | NA |
| All Japonica | 1512 | 79.60% | 3.90% | 3.70% | 12.76% | NA |
| Aus | 269 | 98.50% | 0.00% | 0.00% | 1.49% | NA |
| Indica I | 595 | 94.10% | 0.00% | 0.00% | 5.88% | NA |
| Indica II | 465 | 96.10% | 0.00% | 0.22% | 3.66% | NA |
| Indica III | 913 | 97.90% | 0.10% | 0.11% | 1.86% | NA |
| Indica Intermediate | 786 | 96.70% | 0.00% | 0.51% | 2.80% | NA |
| Temperate Japonica | 767 | 89.00% | 0.30% | 3.78% | 6.91% | NA |
| Tropical Japonica | 504 | 69.40% | 10.10% | 3.57% | 16.87% | NA |
| Japonica Intermediate | 241 | 71.00% | 2.50% | 3.73% | 22.82% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 93.30% | 2.20% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0722028662 | A -> DEL | N | N | silent_mutation | Average:30.25; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| vg0722028662 | A -> G | LOC_Os07g36760.1 | upstream_gene_variant ; 1571.0bp to feature; MODIFIER | silent_mutation | Average:30.25; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| vg0722028662 | A -> G | LOC_Os07g36770.1 | downstream_gene_variant ; 423.0bp to feature; MODIFIER | silent_mutation | Average:30.25; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| vg0722028662 | A -> G | LOC_Os07g36760-LOC_Os07g36770 | intergenic_region ; MODIFIER | silent_mutation | Average:30.25; most accessible tissue: Zhenshan97 panicle, score: 46.362 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0722028662 | NA | 2.88E-07 | mr1156 | 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 |
| vg0722028662 | NA | 4.47E-06 | mr1179 | 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 |
| vg0722028662 | NA | 2.09E-06 | mr1236 | 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 |
| vg0722028662 | 2.17E-07 | 2.17E-07 | mr1663 | Jap_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 |
| vg0722028662 | NA | 3.40E-07 | mr1668 | 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 |