| Variant ID: vg0402529380 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2529380 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, C: 0.33, others allele: 0.00, population size: 88. )
ATCCATCAAAAACTTTTATGAGTTCTTGAATTAACCACTGCATGCAATGCTTCTTCTTCTCCTTCTGCTTCATGTTCTTCTTCTTGTTCACGTCATCATC[C/T]
TTGACTCTCCCATCATCTTCCTTCTTGCCTCTCCCAAGCTTAGGACAATGCGAGCGAAGATGATCAAGTGCACAACACTCAAAACAACGATTCGGTTCTC
GAGAACCGAATCGTTGTTTTGAGTGTTGTGCACTTGATCATCTTCGCTCGCATTGTCCTAAGCTTGGGAGAGGCAAGAAGGAAGATGATGGGAGAGTCAA[G/A]
GATGATGACGTGAACAAGAAGAAGAACATGAAGCAGAAGGAGAAGAAGAAGCATTGCATGCAGTGGTTAATTCAAGAACTCATAAAAGTTTTTGATGGAT
| 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 | 21.70% | 16.60% | 0.59% | 61.13% | NA |
| All Indica | 2759 | 8.40% | 5.80% | 0.87% | 84.85% | NA |
| All Japonica | 1512 | 49.40% | 40.30% | 0.13% | 10.12% | NA |
| Aus | 269 | 3.70% | 0.70% | 0.37% | 95.17% | NA |
| Indica I | 595 | 0.00% | 3.00% | 0.00% | 96.97% | NA |
| Indica II | 465 | 15.50% | 14.20% | 1.08% | 69.25% | NA |
| Indica III | 913 | 8.90% | 1.80% | 1.31% | 88.06% | NA |
| Indica Intermediate | 786 | 10.20% | 7.80% | 0.89% | 81.17% | NA |
| Temperate Japonica | 767 | 24.60% | 74.30% | 0.00% | 1.04% | NA |
| Tropical Japonica | 504 | 72.20% | 3.00% | 0.40% | 24.40% | NA |
| Japonica Intermediate | 241 | 80.50% | 10.40% | 0.00% | 9.13% | NA |
| VI/Aromatic | 96 | 8.30% | 1.00% | 0.00% | 90.62% | NA |
| Intermediate | 90 | 31.10% | 10.00% | 1.11% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402529380 | C -> DEL | LOC_Os04g05104.1 | N | frameshift_variant | Average:15.641; most accessible tissue: Minghui63 flag leaf, score: 30.104 | N | N | N | N |
| vg0402529380 | C -> T | LOC_Os04g05104.1 | synonymous_variant ; p.Lys817Lys; LOW | synonymous_codon | Average:15.641; most accessible tissue: Minghui63 flag leaf, score: 30.104 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402529380 | 1.47E-06 | NA | mr1062 | 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 |
| vg0402529380 | 7.14E-06 | NA | mr1327 | 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 |
| vg0402529380 | 3.01E-06 | 3.79E-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 |
| vg0402529380 | NA | 7.36E-10 | mr1864 | 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 |
| vg0402529380 | NA | 7.51E-08 | mr1521_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 |