| Variant ID: vg0714250056 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14250056 |
| 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: 97. )
CACCTTTAAGTTGATCAAACAAATCATCAATACTAGGCAGTGGATACTTATTCTTGATAGTCACATCGTTAAGTGCACGATAGTCCACACACATCCTCTG[G/A]
GTATGGTCTTTCTTTTCTACAAAGATAACAGGAGCTCCCCATGGAGATGAACTCGGTCTGATGTATCCTTTCTGAAGCAAATCATCTACTTGCCTCTTGA
TCAAGAGGCAAGTAGATGATTTGCTTCAGAAAGGATACATCAGACCGAGTTCATCTCCATGGGGAGCTCCTGTTATCTTTGTAGAAAAGAAAGACCATAC[C/T]
CAGAGGATGTGTGTGGACTATCGTGCACTTAACGATGTGACTATCAAGAATAAGTATCCACTGCCTAGTATTGATGATTTGTTTGATCAACTTAAAGGTG
| 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 | 83.80% | 4.90% | 3.09% | 8.19% | NA |
| All Indica | 2759 | 82.70% | 5.90% | 3.59% | 7.76% | NA |
| All Japonica | 1512 | 83.30% | 4.00% | 2.91% | 9.72% | NA |
| Aus | 269 | 90.70% | 0.00% | 0.74% | 8.55% | NA |
| Indica I | 595 | 89.20% | 3.70% | 1.51% | 5.55% | NA |
| Indica II | 465 | 74.80% | 9.50% | 6.67% | 9.03% | NA |
| Indica III | 913 | 83.50% | 5.90% | 2.63% | 8.00% | NA |
| Indica Intermediate | 786 | 81.60% | 5.60% | 4.45% | 8.40% | NA |
| Temperate Japonica | 767 | 77.10% | 6.80% | 3.91% | 12.26% | NA |
| Tropical Japonica | 504 | 95.60% | 0.20% | 0.60% | 3.57% | NA |
| Japonica Intermediate | 241 | 77.60% | 3.30% | 4.56% | 14.52% | NA |
| VI/Aromatic | 96 | 93.80% | 5.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 3.30% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714250056 | G -> DEL | LOC_Os07g25010.1 | N | frameshift_variant | Average:6.919; most accessible tissue: Callus, score: 21.339 | N | N | N | N |
| vg0714250056 | G -> A | LOC_Os07g25010.1 | synonymous_variant ; p.Thr756Thr; LOW | synonymous_codon | Average:6.919; most accessible tissue: Callus, score: 21.339 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714250056 | NA | 4.51E-09 | mr1624 | 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 |
| vg0714250056 | NA | 7.38E-08 | mr1062_2 | 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 |
| vg0714250056 | NA | 4.30E-06 | mr1726_2 | 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 |
| vg0714250056 | NA | 2.64E-07 | mr1733_2 | 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 |
| vg0714250056 | NA | 4.71E-06 | mr1741_2 | 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 |