| Variant ID: vg0400672500 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 672500 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 126. )
CGGCAACTTACAACAAAAAGGTTCGACCGACGGAGCTGTTGCCTGGTCATCTTGTCCTAAGAAAGAAGGTGAACCCGATAGCCGTTGGCAAGCTTGAATC[G/A]
AAGTGGGAAGGACCGTACCTCATCAAGCACAAGTCCAAGACGGGGTCCTTTCGACTGGCGACACTGGAAGGCGAAGAGTTCGACCATTCCTGGAACGCTG
CAGCGTTCCAGGAATGGTCGAACTCTTCGCCTTCCAGTGTCGCCAGTCGAAAGGACCCCGTCTTGGACTTGTGCTTGATGAGGTACGGTCCTTCCCACTT[C/T]
GATTCAAGCTTGCCAACGGCTATCGGGTTCACCTTCTTTCTTAGGACAAGATGACCAGGCAACAGCTCCGTCGGTCGAACCTTTTTGTTGTAAGTTGCCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.40% | 3.40% | 3.24% | 0.00% | NA |
| All Indica | 2759 | 88.90% | 5.60% | 5.47% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 87.40% | 1.00% | 11.60% | 0.00% | NA |
| Indica II | 465 | 75.10% | 16.30% | 8.60% | 0.00% | NA |
| Indica III | 913 | 98.80% | 1.00% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 86.90% | 8.00% | 5.09% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0400672500 | G -> A | LOC_Os04g02080.1 | synonymous_variant ; p.Ser443Ser; LOW | synonymous_codon | Average:49.124; most accessible tissue: Zhenshan97 flag leaf, score: 70.007 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0400672500 | NA | 6.62E-06 | 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 |
| vg0400672500 | NA | 2.71E-09 | mr1565 | 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 |
| vg0400672500 | NA | 5.42E-08 | mr1715 | 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 |
| vg0400672500 | NA | 9.57E-08 | mr1771 | 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 |