| Variant ID: vg1217936768 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17936768 |
| 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: 272. )
ACGCTATTTATCTCTCATATTCACCTGAAAATTAATAATTTAATGGGCGTAATGTCTACTAGCAAATAACCACGTTTAGATAGTGTTTTTCCCCAAAAGT[G/A]
AATTCGTGCGGTGTCCGACTGGTAAAATCACAAAGTCTTGATGTCCTGTAGCAAAGTTTGCCTAATTTTTATGTTTTTAGTTTCATCATGAGAAATACTT
AAGTATTTCTCATGATGAAACTAAAAACATAAAAATTAGGCAAACTTTGCTACAGGACATCAAGACTTTGTGATTTTACCAGTCGGACACCGCACGAATT[C/T]
ACTTTTGGGGAAAAACACTATCTAAACGTGGTTATTTGCTAGTAGACATTACGCCCATTAAATTATTAATTTTCAGGTGAATATGAGAGATAAATAGCGT
| 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 | 79.80% | 20.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 71.70% | 28.30% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.60% | 9.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 61.50% | 38.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 63.40% | 36.50% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 72.90% | 27.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 90.50% | 9.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 65.60% | 34.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1217936768 | G -> A | LOC_Os12g30000.1 | downstream_gene_variant ; 2409.0bp to feature; MODIFIER | silent_mutation | Average:70.486; most accessible tissue: Minghui63 panicle, score: 87.238 | N | N | N | N |
| vg1217936768 | G -> A | LOC_Os12g29990-LOC_Os12g30000 | intergenic_region ; MODIFIER | silent_mutation | Average:70.486; most accessible tissue: Minghui63 panicle, score: 87.238 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217936768 | 3.01E-07 | NA | mr1024 | 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 |
| vg1217936768 | 7.83E-06 | 7.83E-06 | mr1024 | 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 |
| vg1217936768 | NA | 1.68E-06 | mr1705_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 |