| Variant ID: vg0431240137 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 31240137 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 281. )
GCTTACTCCTATGTGAACTTGACCTGTTTTTGTTTCTAACGGTTCTTCATTTTCCTTCAGAGCGCATTGCTTCTACTGAGGTTGTAAGAGTACAACCACC[T/C]
GCACCCCCAGTTGCTGTGTCTCGTAGTGGCACGCGTGTGCCAATGCGAAGACCTGATGGTGGAGGCTCAGTATCGAAAGCCAAGGTCAAATTGTTGGTGA
TCACCAACAATTTGACCTTGGCTTTCGATACTGAGCCTCCACCATCAGGTCTTCGCATTGGCACACGCGTGCCACTACGAGACACAGCAACTGGGGGTGC[A/G]
GGTGGTTGTACTCTTACAACCTCAGTAGAAGCAATGCGCTCTGAAGGAAAATGAAGAACCGTTAGAAACAAAAACAGGTCAAGTTCACATAGGAGTAAGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.70% | 6.30% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 97.30% | 2.70% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 86.00% | 14.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.00% | 5.90% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 73.80% | 26.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0431240137 | T -> C | LOC_Os04g52540.1 | synonymous_variant ; p.Pro178Pro; LOW | synonymous_codon | Average:57.821; most accessible tissue: Zhenshan97 flower, score: 75.428 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0431240137 | NA | 3.12E-06 | mr1318 | 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 |
| vg0431240137 | NA | 1.03E-06 | mr1788 | 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 |
| vg0431240137 | NA | 3.04E-06 | mr1062_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 |