| Variant ID: vg0825559450 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 25559450 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 154. )
TGCTCCCATCGTACTTTTCTATTGCCCCCGGTCGGAACCTCTCAGGCCATCGGACATCGCGCAACGAACGACCGAAAGCCCTACACCCAGCACTAGGGGC[G/A]
GTGGGTTGTCGGCGATCGTATGTCCTTCGTGGATGTCTGTCTGACGATGAGGAGGAGGAAGAAGATAAGGACGACGATGGGTCGCTTGGTTCCGGTGTAG
CTACACCGGAACCAAGCGACCCATCGTCGTCCTTATCTTCTTCCTCCTCCTCATCGTCAGACAGACATCCACGAAGGACATACGATCGCCGACAACCCAC[C/T]
GCCCCTAGTGCTGGGTGTAGGGCTTTCGGTCGTTCGTTGCGCGATGTCCGATGGCCTGAGAGGTTCCGACCGGGGGCAATAGAAAAGTACGATGGGAGCA
| 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 | 45.40% | 41.70% | 3.81% | 9.08% | NA |
| All Indica | 2759 | 20.30% | 61.00% | 4.64% | 14.06% | NA |
| All Japonica | 1512 | 97.30% | 1.30% | 0.13% | 1.32% | NA |
| Aus | 269 | 1.90% | 82.50% | 15.24% | 0.37% | NA |
| Indica I | 595 | 37.60% | 30.30% | 5.55% | 26.55% | NA |
| Indica II | 465 | 15.10% | 53.30% | 5.38% | 26.24% | NA |
| Indica III | 913 | 12.30% | 85.50% | 1.31% | 0.88% | NA |
| Indica Intermediate | 786 | 19.50% | 60.40% | 7.38% | 12.72% | NA |
| Temperate Japonica | 767 | 97.90% | 1.00% | 0.26% | 0.78% | NA |
| Tropical Japonica | 504 | 98.40% | 0.60% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 92.90% | 3.30% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 71.90% | 13.50% | 6.25% | 8.33% | NA |
| Intermediate | 90 | 47.80% | 35.60% | 3.33% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825559450 | G -> A | LOC_Os08g40370.1 | synonymous_variant ; p.Thr318Thr; LOW | synonymous_codon | Average:29.136; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | N | N | N | N |
| vg0825559450 | G -> DEL | LOC_Os08g40370.1 | N | frameshift_variant | Average:29.136; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0825559450 | 2.57E-07 | NA | mr1874 | 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 |
| vg0825559450 | 4.08E-09 | 9.11E-13 | mr1874 | 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 |
| vg0825559450 | NA | 1.08E-07 | mr1170_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 |
| vg0825559450 | 4.93E-06 | 2.73E-12 | mr1874_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 |
| vg0825559450 | NA | 7.58E-06 | mr1882_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 |