| Variant ID: vg1124745257 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24745257 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 127. )
CAACAGGTACAGGGGGGTTTGATAGGTAGCGCTTGAGTGCAAGAAATGCCTCTTCGGCTTCCTGTGTCCATACAAATTTGTCTTGCTTCTTCAGCAGAGC[G/A]
AAGAAGGGTTGTCCTCGTTCTCCCATCCTAGCGATGAACATGCTTAGTGCTGCCATGCATCCGGTTAGCTTTTGTACTTCCTTGAGTCTTGTGGGCGACT
AGTCGCCCACAAGACTCAAGGAAGTACAAAAGCTAACCGGATGCATGGCAGCACTAAGCATGTTCATCGCTAGGATGGGAGAACGAGGACAACCCTTCTT[C/T]
GCTCTGCTGAAGAAGCAAGACAAATTTGTATGGACACAGGAAGCCGAAGAGGCATTTCTTGCACTCAAGCGCTACCTATCAAACCCCCCTGTACCTGTTG
| 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 | 93.20% | 1.30% | 1.84% | 3.60% | NA |
| All Indica | 2759 | 94.30% | 2.00% | 2.57% | 1.05% | NA |
| All Japonica | 1512 | 90.60% | 0.20% | 0.73% | 8.47% | NA |
| Aus | 269 | 96.30% | 0.00% | 0.00% | 3.72% | NA |
| Indica I | 595 | 90.30% | 3.70% | 5.38% | 0.67% | NA |
| Indica II | 465 | 88.20% | 3.70% | 3.66% | 4.52% | NA |
| Indica III | 913 | 99.20% | 0.40% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 95.40% | 1.70% | 2.54% | 0.38% | NA |
| Temperate Japonica | 767 | 96.70% | 0.40% | 0.65% | 2.22% | NA |
| Tropical Japonica | 504 | 81.00% | 0.00% | 0.79% | 18.25% | NA |
| Japonica Intermediate | 241 | 91.30% | 0.00% | 0.83% | 7.88% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 5.56% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1124745257 | G -> A | LOC_Os11g41280.1 | synonymous_variant ; p.Phe811Phe; LOW | synonymous_codon | Average:37.586; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
| vg1124745257 | G -> DEL | LOC_Os11g41280.1 | N | frameshift_variant | Average:37.586; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124745257 | 1.48E-07 | 1.20E-07 | mr1123 | 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 |
| vg1124745257 | NA | 1.40E-06 | mr1191_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 |
| vg1124745257 | NA | 7.26E-08 | mr1662_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 |
| vg1124745257 | NA | 6.37E-08 | mr1662_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 |