| Variant ID: vg1204091810 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4091810 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, C: 0.03, others allele: 0.00, population size: 122. )
GATCATCTCTTCAGTCGAAGCTCGATGACCGGCTCCATCTCCCCTTCATGTACTCCTCCAGCGACACGTTCGCCGCCGTGAAGTCGGCGCCGCCGCTGCT[G/C]
ACGGACGCCGAGTCGTCGTCGACGTCGAGCAGCGCAAGGTTAATGTACGACTGGATGTCCTTCTTCTCCGGCGAAGCGCCATCGCCATCGTCGGTGTCAT
ATGACACCGACGATGGCGATGGCGCTTCGCCGGAGAAGAAGGACATCCAGTCGTACATTAACCTTGCGCTGCTCGACGTCGACGACGACTCGGCGTCCGT[C/G]
AGCAGCGGCGGCGCCGACTTCACGGCGGCGAACGTGTCGCTGGAGGAGTACATGAAGGGGAGATGGAGCCGGTCATCGAGCTTCGACTGAAGAGATGATC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.90% | 0.60% | 6.98% | 40.52% | NA |
| All Indica | 2759 | 32.90% | 0.80% | 6.60% | 59.73% | NA |
| All Japonica | 1512 | 84.10% | 0.10% | 4.37% | 11.44% | NA |
| Aus | 269 | 44.20% | 2.20% | 29.00% | 24.54% | NA |
| Indica I | 595 | 15.10% | 0.70% | 9.92% | 74.29% | NA |
| Indica II | 465 | 23.70% | 0.60% | 3.44% | 72.26% | NA |
| Indica III | 913 | 47.30% | 0.80% | 5.59% | 46.33% | NA |
| Indica Intermediate | 786 | 35.00% | 1.00% | 7.12% | 56.87% | NA |
| Temperate Japonica | 767 | 94.40% | 0.00% | 0.78% | 4.82% | NA |
| Tropical Japonica | 504 | 81.90% | 0.40% | 5.95% | 11.71% | NA |
| Japonica Intermediate | 241 | 55.60% | 0.00% | 12.45% | 31.95% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 4.17% | 5.21% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 0.00% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204091810 | G -> C | LOC_Os12g08050.1 | synonymous_variant ; p.Val278Val; LOW | synonymous_codon | Average:48.396; most accessible tissue: Minghui63 root, score: 71.702 | N | N | N | N |
| vg1204091810 | G -> DEL | LOC_Os12g08050.1 | N | frameshift_variant | Average:48.396; most accessible tissue: Minghui63 root, score: 71.702 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204091810 | NA | 5.04E-08 | mr1693 | 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 |
| vg1204091810 | 8.27E-06 | 1.23E-07 | mr1679_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 |
| vg1204091810 | 1.51E-06 | 1.66E-10 | mr1691_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 |
| vg1204091810 | 3.68E-08 | 3.37E-11 | mr1720_2 | 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 |