| Variant ID: vg0410881366 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10881366 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGCTCAAATAAAACACACCTCTCTCTTTCCCCTCAAGCTCCTGAATCAAAACTGAGTCGATTGACTTCTCACCGGCCAAGAGATATAATCTGAAAGGAAT[C/T]
CCCTTCTGTGGCGGGATTAAAACTGGAGGAGAACTAAGATATGCTTTAATATTATCCAAAGCCTTATGCTGTTCTACCCCCCAGGTGAATTCTTGATCGG
CCGATCAAGAATTCACCTGGGGGGTAGAACAGCATAAGGCTTTGGATAATATTAAAGCATATCTTAGTTCTCCTCCAGTTTTAATCCCGCCACAGAAGGG[G/A]
ATTCCTTTCAGATTATATCTCTTGGCCGGTGAGAAGTCAATCGACTCAGTTTTGATTCAGGAGCTTGAGGGGAAAGAGAGAGGTGTGTTTTATTTGAGCC
| 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 | 79.30% | 6.60% | 5.88% | 8.19% | NA |
| All Indica | 2759 | 70.00% | 9.60% | 7.65% | 12.72% | NA |
| All Japonica | 1512 | 96.10% | 0.90% | 2.05% | 0.99% | NA |
| Aus | 269 | 91.40% | 3.70% | 3.72% | 1.12% | NA |
| Indica I | 595 | 78.80% | 3.40% | 4.03% | 13.78% | NA |
| Indica II | 465 | 74.80% | 4.70% | 8.39% | 12.04% | NA |
| Indica III | 913 | 55.90% | 20.50% | 9.97% | 13.69% | NA |
| Indica Intermediate | 786 | 77.00% | 4.60% | 7.25% | 11.20% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 90.90% | 2.40% | 4.96% | 1.79% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.40% | 2.49% | 1.66% | NA |
| VI/Aromatic | 96 | 44.80% | 20.80% | 22.92% | 11.46% | NA |
| Intermediate | 90 | 84.40% | 3.30% | 4.44% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410881366 | C -> DEL | LOC_Os04g19540.1 | N | frameshift_variant | Average:31.04; most accessible tissue: Minghui63 young leaf, score: 48.378 | N | N | N | N |
| vg0410881366 | C -> T | LOC_Os04g19540.1 | synonymous_variant ; p.Gly550Gly; LOW | synonymous_codon | Average:31.04; most accessible tissue: Minghui63 young leaf, score: 48.378 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0410881366 | NA | 7.76E-07 | mr1277_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 |