| Variant ID: vg0714251445 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14251445 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, others allele: 0.00, population size: 41. )
ACTCCTTCTTCTTGAGGGACACCACTCCCGATGGTATATGCGTCTTGCGCAAAGCAGCGGTGAACTCAAGCCAAGAGATAGGTTCAGCAGTAGTCCTGTT[A/G]
AGGCAGGAGTGATCCCACCATTCCGAAGCAGGGCCATGCAGCTGGTGTGACGCAAAAGAGACCTTCTCCTGGTCTCTGCACTGGAGCAGATCCAACTTCT
AGAAGTTGGATCTGCTCCAGTGCAGAGACCAGGAGAAGGTCTCTTTTGCGTCACACCAGCTGCATGGCCCTGCTTCGGAATGGTGGGATCACTCCTGCCT[T/C]
AACAGGACTACTGCTGAACCTATCTCTTGGCTTGAGTTCACCGCTGCTTTGCGCAAGACGCATATACCATCGGGAGTGGTGTCCCTCAAGAAGAAGGAGT
| 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 | 53.50% | 16.00% | 4.72% | 25.75% | NA |
| All Indica | 2759 | 42.40% | 24.40% | 2.72% | 30.45% | NA |
| All Japonica | 1512 | 72.40% | 5.00% | 8.86% | 13.69% | NA |
| Aus | 269 | 43.50% | 1.10% | 2.97% | 52.42% | NA |
| Indica I | 595 | 47.10% | 16.60% | 2.69% | 33.61% | NA |
| Indica II | 465 | 52.50% | 27.30% | 3.01% | 17.20% | NA |
| Indica III | 913 | 29.40% | 29.60% | 2.63% | 38.44% | NA |
| Indica Intermediate | 786 | 48.10% | 22.60% | 2.67% | 26.59% | NA |
| Temperate Japonica | 767 | 76.00% | 3.40% | 7.69% | 12.91% | NA |
| Tropical Japonica | 504 | 73.00% | 3.20% | 9.72% | 14.09% | NA |
| Japonica Intermediate | 241 | 59.80% | 14.10% | 10.79% | 15.35% | NA |
| VI/Aromatic | 96 | 85.40% | 1.00% | 1.04% | 12.50% | NA |
| Intermediate | 90 | 71.10% | 4.40% | 5.56% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714251445 | A -> DEL | LOC_Os07g25010.1 | N | frameshift_variant | Average:12.217; most accessible tissue: Callus, score: 44.508 | N | N | N | N |
| vg0714251445 | A -> G | LOC_Os07g25010.1 | synonymous_variant ; p.Leu346Leu; LOW | synonymous_codon | Average:12.217; most accessible tissue: Callus, score: 44.508 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714251445 | 5.70E-07 | 7.47E-11 | mr1053 | 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 |
| vg0714251445 | 1.53E-07 | 8.38E-09 | mr1053 | 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 |
| vg0714251445 | 4.21E-06 | 1.78E-06 | mr1070 | 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 |
| vg0714251445 | 1.03E-06 | NA | mr1128 | 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 |
| vg0714251445 | 5.64E-07 | 1.00E-07 | mr1128 | 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 |
| vg0714251445 | 1.04E-06 | NA | mr1147 | 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 |
| vg0714251445 | 2.54E-08 | 1.63E-08 | mr1147 | 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 |
| vg0714251445 | NA | 3.93E-06 | mr1283 | 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 |
| vg0714251445 | NA | 1.81E-07 | mr1913 | 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 |