| Variant ID: vg0414121081 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14121081 |
| 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: 300. )
CACGGGATCGAACATTGCGATTATGATAACGCCGCAACCCTTGTAAGTATCGAGCCGAGCGAATCAAAGCTGCTTCGCGGACTTCTTCCAATCGATGCAA[G/A]
TCATCCACTCGGTCCTCTTCGTAACGTTCTTCACGGAAATTTCGAAAGCGCAAAGATTCGAATTCAACTTCACTCGGCAACATTGCTTCTGCCCCATAGA
TCTATGGGGCAGAAGCAATGTTGCCGAGTGAAGTTGAATTCGAATCTTTGCGCTTTCGAAATTTCCGTGAAGAACGTTACGAAGAGGACCGAGTGGATGA[C/T]
TTGCATCGATTGGAAGAAGTCCGCGAAGCAGCTTTGATTCGCTCGGCTCGATACTTACAAGGGTTGCGGCGTTATCATAATCGCAATGTTCGATCCCGTG
| 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 | 90.50% | 5.30% | 2.01% | 2.16% | NA |
| All Indica | 2759 | 95.90% | 0.70% | 1.70% | 1.67% | NA |
| All Japonica | 1512 | 79.40% | 15.10% | 2.45% | 2.98% | NA |
| Aus | 269 | 95.20% | 0.00% | 1.12% | 3.72% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 80.60% | 2.80% | 7.53% | 9.03% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.50% | 0.60% | 1.40% | 0.51% | NA |
| Temperate Japonica | 767 | 97.40% | 0.80% | 1.17% | 0.65% | NA |
| Tropical Japonica | 504 | 57.50% | 34.30% | 3.97% | 4.17% | NA |
| Japonica Intermediate | 241 | 68.00% | 20.70% | 3.32% | 7.88% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 3.30% | 6.67% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414121081 | G -> DEL | LOC_Os04g24590.1 | N | frameshift_variant | Average:27.726; most accessible tissue: Minghui63 flag leaf, score: 44.406 | N | N | N | N |
| vg0414121081 | G -> A | LOC_Os04g24590.1 | synonymous_variant ; p.Asp1895Asp; LOW | synonymous_codon | Average:27.726; most accessible tissue: Minghui63 flag leaf, score: 44.406 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0414121081 | 2.48E-06 | 2.48E-06 | mr1068 | 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 |
| vg0414121081 | NA | 2.10E-06 | mr1090 | 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 |
| vg0414121081 | NA | 5.02E-07 | mr1403 | 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 |
| vg0414121081 | 1.26E-06 | 1.26E-06 | mr1526 | 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 |
| vg0414121081 | 8.27E-07 | 8.27E-07 | mr1945 | 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 |