| Variant ID: vg0404000463 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4000463 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 100. )
TCTGAGGTATCAAAACCATAAGGTTGGAGGGAAACACCACATCCCTAAGATGAATAGGTACGTCGATGCAAGCATGGCTTACGGTTACCTCACCCCCAGG[C/T]
GAGTGTACTATCATAGGCTTTCTAACTCCTACCAGAGTTAAGTTGTGCTGTTGACTAGCCTCCAGGGATATGAATGAATGCGATGCACCAGAATCGAGGA
TCCTCGATTCTGGTGCATCGCATTCATTCATATCCCTGGAGGCTAGTCAACAGCACAACTTAACTCTGGTAGGAGTTAGAAAGCCTATGATAGTACACTC[G/A]
CCTGGGGGTGAGGTAACCGTAAGCCATGCTTGCATCGACGTACCTATTCATCTTAGGGATGTGGTGTTTCCCTCCAACCTTATGGTTTTGATACCTCAGA
| 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 | 46.00% | 43.50% | 4.59% | 5.95% | NA |
| All Indica | 2759 | 26.40% | 67.10% | 5.91% | 0.62% | NA |
| All Japonica | 1512 | 76.30% | 3.60% | 2.71% | 17.33% | NA |
| Aus | 269 | 55.00% | 42.40% | 2.60% | 0.00% | NA |
| Indica I | 595 | 44.40% | 52.40% | 3.19% | 0.00% | NA |
| Indica II | 465 | 34.60% | 55.10% | 9.68% | 0.65% | NA |
| Indica III | 913 | 8.50% | 84.80% | 6.13% | 0.55% | NA |
| Indica Intermediate | 786 | 28.80% | 64.60% | 5.47% | 1.15% | NA |
| Temperate Japonica | 767 | 69.10% | 0.90% | 1.96% | 28.03% | NA |
| Tropical Japonica | 504 | 84.30% | 6.50% | 3.77% | 5.36% | NA |
| Japonica Intermediate | 241 | 82.60% | 6.20% | 2.90% | 8.30% | NA |
| VI/Aromatic | 96 | 95.80% | 2.10% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 55.60% | 37.80% | 6.67% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404000463 | C -> DEL | LOC_Os04g07510.1 | N | frameshift_variant | Average:12.918; most accessible tissue: Callus, score: 57.086 | N | N | N | N |
| vg0404000463 | C -> T | LOC_Os04g07510.1 | synonymous_variant ; p.Ser348Ser; LOW | synonymous_codon | Average:12.918; most accessible tissue: Callus, score: 57.086 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404000463 | 7.00E-06 | NA | mr1120 | 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 |
| vg0404000463 | NA | 1.03E-07 | mr1557 | 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 |
| vg0404000463 | NA | 7.06E-07 | mr1715 | 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 |
| vg0404000463 | NA | 1.95E-06 | mr1540_2 | 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 |