| Variant ID: vg0100448187 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 448187 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 124. )
AATCCAATTACTTAACCCGCCTTCCACTTTGAACGGAAGCTGAAACCAAATCTGTGGGTTTGACTCATTTACCATCCTGGGTCCACCAAGATACTTGGCA[T/A]
CATGCTAGTAATGATTACCACGCCATGCTACTCGTACTTAGTTAAAGTGCGAAGACATTGTGTGTAGGCCTTTAGGGAAGTATTGGGAAAGAATGGTTAT
ATAACCATTCTTTCCCAATACTTCCCTAAAGGCCTACACACAATGTCTTCGCACTTTAACTAAGTACGAGTAGCATGGCGTGGTAATCATTACTAGCATG[A/T]
TGCCAAGTATCTTGGTGGACCCAGGATGGTAAATGAGTCAAACCCACAGATTTGGTTTCAGCTTCCGTTCAAAGTGGAAGGCGGGTTAAGTAATTGGATT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.90% | 9.40% | 10.56% | 24.14% | NA |
| All Indica | 2759 | 31.20% | 14.80% | 15.95% | 38.09% | NA |
| All Japonica | 1512 | 92.30% | 1.70% | 2.38% | 3.70% | NA |
| Aus | 269 | 87.00% | 1.50% | 4.83% | 6.69% | NA |
| Indica I | 595 | 1.70% | 16.10% | 27.56% | 54.62% | NA |
| Indica II | 465 | 34.40% | 13.50% | 9.89% | 42.15% | NA |
| Indica III | 913 | 47.20% | 15.10% | 9.31% | 28.37% | NA |
| Indica Intermediate | 786 | 33.10% | 14.00% | 18.45% | 34.48% | NA |
| Temperate Japonica | 767 | 87.20% | 2.70% | 3.78% | 6.26% | NA |
| Tropical Japonica | 504 | 98.40% | 0.40% | 0.60% | 0.60% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.80% | 1.66% | 2.07% | NA |
| VI/Aromatic | 96 | 92.70% | 2.10% | 1.04% | 4.17% | NA |
| Intermediate | 90 | 72.20% | 4.40% | 10.00% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100448187 | T -> A | LOC_Os01g01830.1 | intron_variant ; MODIFIER | silent_mutation | Average:56.032; most accessible tissue: Callus, score: 83.36 | N | N | N | N |
| vg0100448187 | T -> DEL | N | N | silent_mutation | Average:56.032; most accessible tissue: Callus, score: 83.36 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100448187 | NA | 1.54E-09 | mr1260 | 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 |
| vg0100448187 | NA | 2.56E-15 | mr1531 | 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 |
| vg0100448187 | NA | 1.02E-13 | mr1807 | 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 |
| vg0100448187 | NA | 9.03E-20 | mr1870 | 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 |
| vg0100448187 | NA | 3.66E-20 | mr1870_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 |