| Variant ID: vg0427936017 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 27936017 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTGCGCAACATCAAGCCGGAAGACAAGTTCCTTCGCCATCTGAAGCTGCAGACGAACACTGCCAATGTGACGGTCACTCCAGCTCTGTAAGCGCTTGGCC[A/G]
TGGTAGAGAAGCACCAAGCAAGAGCGGCAAGAGGGGGTAGGTTGGCAGGGGGATGCCAGGCGTCCTACACGACTTGAAGAAAGCCGTCGAACTTGGGCCA
TGGCCCAAGTTCGACGGCTTTCTTCAAGTCGTGTAGGACGCCTGGCATCCCCCTGCCAACCTACCCCCTCTTGCCGCTCTTGCTTGGTGCTTCTCTACCA[T/C]
GGCCAAGCGCTTACAGAGCTGGAGTGACCGTCACATTGGCAGTGTTCGTCTGCAGCTTCAGATGGCGAAGGAACTTGTCTTCCGGCTTGATGTTGCGCAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.20% | 1.60% | 15.19% | 35.02% | NA |
| All Indica | 2759 | 18.10% | 2.60% | 20.77% | 58.54% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.13% | 0.40% | NA |
| Aus | 269 | 43.50% | 1.50% | 49.81% | 5.20% | NA |
| Indica I | 595 | 18.00% | 2.20% | 10.76% | 69.08% | NA |
| Indica II | 465 | 8.80% | 2.60% | 21.72% | 66.88% | NA |
| Indica III | 913 | 20.90% | 3.10% | 25.74% | 50.27% | NA |
| Indica Intermediate | 786 | 20.40% | 2.40% | 22.01% | 55.22% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 10.00% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0427936017 | A -> DEL | N | N | silent_mutation | Average:9.732; most accessible tissue: Minghui63 young leaf, score: 16.99 | N | N | N | N |
| vg0427936017 | A -> G | LOC_Os04g47059.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.732; most accessible tissue: Minghui63 young leaf, score: 16.99 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0427936017 | 3.14E-07 | 6.68E-41 | mr1873 | 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 |
| vg0427936017 | 1.68E-06 | 3.08E-09 | mr1873 | 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 |
| vg0427936017 | NA | 5.40E-33 | mr1873_2 | 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 |
| vg0427936017 | NA | 3.57E-07 | mr1873_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 |