| Variant ID: vg0714029010 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14029010 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCCCTGTTAACTCAGTTCCTGCAACAGTGCTTTTCGATTCTGGTGCTACGCATTCATTTTTATCTATGAGTTTTGCGGGAAATCATGTGATGGAAGTAGA[A/G]
GAGCTTAGACGTCCTTTGATGGTTAGTACCCCAAGTAACCAAGCACTCTCATCACAACGTAGCCCCTCTGTCAGAATAGAGATCCAAGGTGTACCCTCCC
GGGAGGGTACACCTTGGATCTCTATTCTGACAGAGGGGCTACGTTGTGATGAGAGTGCTTGGTTACTTGGGGTACTAACCATCAAAGGACGTCTAAGCTC[T/C]
TCTACTTCCATCACATGATTTCCCGCAAAACTCATAGATAAAAATGAATGCGTAGCACCAGAATCGAAAAGCACTGTTGCAGGAACTGAGTTAACAGGGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.80% | 4.10% | 9.20% | 3.91% | NA |
| All Indica | 2759 | 76.30% | 6.60% | 14.21% | 2.90% | NA |
| All Japonica | 1512 | 90.50% | 0.50% | 2.38% | 6.68% | NA |
| Aus | 269 | 97.40% | 0.00% | 1.12% | 1.49% | NA |
| Indica I | 595 | 92.80% | 0.70% | 3.87% | 2.69% | NA |
| Indica II | 465 | 66.20% | 15.30% | 14.41% | 4.09% | NA |
| Indica III | 913 | 69.30% | 5.70% | 22.45% | 2.52% | NA |
| Indica Intermediate | 786 | 78.00% | 6.90% | 12.34% | 2.80% | NA |
| Temperate Japonica | 767 | 90.10% | 0.40% | 1.56% | 7.95% | NA |
| Tropical Japonica | 504 | 98.00% | 0.00% | 0.20% | 1.79% | NA |
| Japonica Intermediate | 241 | 75.90% | 1.70% | 9.54% | 12.86% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 4.40% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714029010 | A -> DEL | LOC_Os07g24660.1 | N | frameshift_variant | Average:14.175; most accessible tissue: Callus, score: 30.902 | N | N | N | N |
| vg0714029010 | A -> G | LOC_Os07g24660.1 | synonymous_variant ; p.Glu625Glu; LOW | synonymous_codon | Average:14.175; most accessible tissue: Callus, score: 30.902 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714029010 | NA | 4.82E-06 | mr1354_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 |
| vg0714029010 | 2.46E-06 | NA | mr1902_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 |