| Variant ID: vg0500820450 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 820450 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, G: 0.22, others allele: 0.00, population size: 99. )
TGTCGGTTTTAAGACAAAGGTGCCGGTTTTTTAAAAACCGACACCTATAATAAATTAAAGGTACCGGTTTTGGGTAAAAAAAACCAACACCTTTACGGAT[C/G]
GAGCCGAGCCGGCTGAGCCGACCGGCGGGCCCCACAACCATCGGATAAGGTCATCTCGCTCAGCCTCTCCTCTCCTCTCTCTCTCTCTCTCCCTTCTCTC
GAGAGAAGGGAGAGAGAGAGAGAGAGGAGAGGAGAGGCTGAGCGAGATGACCTTATCCGATGGTTGTGGGGCCCGCCGGTCGGCTCAGCCGGCTCGGCTC[G/C]
ATCCGTAAAGGTGTTGGTTTTTTTTACCCAAAACCGGTACCTTTAATTTATTATAGGTGTCGGTTTTTAAAAAACCGGCACCTTTGTCTTAAAACCGACA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.10% | 34.40% | 0.49% | 0.02% | NA |
| All Indica | 2759 | 47.60% | 51.80% | 0.58% | 0.04% | NA |
| All Japonica | 1512 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 73.20% | 24.90% | 1.86% | 0.00% | NA |
| Indica I | 595 | 68.40% | 31.40% | 0.17% | 0.00% | NA |
| Indica II | 465 | 62.60% | 36.80% | 0.43% | 0.22% | NA |
| Indica III | 913 | 19.90% | 79.40% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 55.20% | 43.90% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 32.30% | 65.60% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 23.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0500820450 | C -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500820450 | C -> G | LOC_Os05g02435.1 | upstream_gene_variant ; 1095.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0500820450 | C -> G | LOC_Os05g02430-LOC_Os05g02435 | intergenic_region ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0500820450 | NA | 5.57E-06 | mr1729 | 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 |
| vg0500820450 | 3.29E-06 | 6.26E-07 | mr1754 | 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 |
| vg0500820450 | NA | 2.64E-06 | mr1807 | 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 |
| vg0500820450 | NA | 6.28E-06 | mr1020_2 | 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 |
| vg0500820450 | NA | 1.72E-06 | mr1807_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 |