| Variant ID: vg0727277278 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 27277278 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACCGCGAAGCAAACGGACGGATTGCAAAGTGGGCTTTGGAGTTGATGTCTTTGGACATATCATTCAAGGCCCGAATTTCGATCAAGTCCCAGGCGTTAGC[C/T]
GATTTTGTCGCCGAATGGACCGAGTGCCAGGAGGATACCCCCGCGGAGAAGATGGAGCACTGGACCATGCATTTTGACGGATCAAAACGACTTTCGGGCA
TGCCCGAAAGTCGTTTTGATCCGTCAAAATGCATGGTCCAGTGCTCCATCTTCTCCGCGGGGGTATCCTCCTGGCACTCGGTCCATTCGGCGACAAAATC[G/A]
GCTAACGCCTGGGACTTGATCGAAATTCGGGCCTTGAATGATATGTCCAAAGACATCAACTCCAAAGCCCACTTTGCAATCCGTCCGTTTGCTTCGCGGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.50% | 1.20% | 7.34% | 0.00% | NA |
| All Indica | 2759 | 87.60% | 1.70% | 10.73% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Aus | 269 | 79.60% | 3.30% | 17.10% | 0.00% | NA |
| Indica I | 595 | 82.20% | 1.50% | 16.30% | 0.00% | NA |
| Indica II | 465 | 91.60% | 0.40% | 7.96% | 0.00% | NA |
| Indica III | 913 | 88.70% | 3.00% | 8.32% | 0.00% | NA |
| Indica Intermediate | 786 | 87.90% | 1.10% | 10.94% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0727277278 | C -> T | LOC_Os07g45680.1 | synonymous_variant ; p.Ala1374Ala; LOW | synonymous_codon | Average:45.212; most accessible tissue: Minghui63 flag leaf, score: 70.17 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0727277278 | 1.73E-06 | NA | mr1057 | 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 |
| vg0727277278 | 2.85E-06 | 2.85E-06 | mr1384 | 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 |
| vg0727277278 | 6.93E-06 | NA | mr1410 | 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 |
| vg0727277278 | 2.42E-06 | 2.42E-06 | mr1631 | 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 |