| Variant ID: vg0710362096 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10362096 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ACATCGCAGCAGGAAAACAGTGTTTGATATGGTTAAAGATCTTAAAGTAATGTTCGAAAAGGGGCCTGGAAGCCAGCCTATAGAGAGCGAAGATGGTCAC[G/A]
CGGCGATGTGGAAAAAGAACTCTATATTTTGGGAGTTATCCTATTGGGAATTCTTGGATGTCCGCCACACAATTGACGTGATGCACCTCACTAAGACCTT
AAGGTCTTAGTGAGGTGCATCACGTCAATTGTGTGGCGGACATCCAAGAATTCCCAATAGGATAACTCCCAAAATATAGAGTTCTTTTTCCACATCGCCG[C/T]
GTGACCATCTTCGCTCTCTATAGGCTGGCTTCCAGGCCCCTTTTCGAACATTACTTTAAGATCTTTAACCATATCAAACACTGTTTTCCTGCTGCGATGT
| 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 | 59.00% | 39.70% | 0.02% | 1.29% | NA |
| All Indica | 2759 | 93.80% | 6.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 1.80% | 95.40% | 0.00% | 2.84% | NA |
| Aus | 269 | 41.30% | 58.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.70% | 4.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 88.00% | 12.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 1.80% | 98.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.80% | 89.90% | 0.00% | 8.33% | NA |
| Japonica Intermediate | 241 | 1.70% | 97.90% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 15.60% | 66.70% | 0.00% | 17.71% | NA |
| Intermediate | 90 | 51.10% | 47.80% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710362096 | G -> DEL | N | N | silent_mutation | Average:19.042; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0710362096 | G -> A | LOC_Os07g17530.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:19.042; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0710362096 | G -> A | LOC_Os07g17540.1 | upstream_gene_variant ; 4923.0bp to feature; MODIFIER | silent_mutation | Average:19.042; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0710362096 | 3.34E-06 | 2.59E-06 | mr1236_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 |
| vg0710362096 | 1.64E-06 | 1.64E-06 | mr1967_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 |