| Variant ID: vg1214645996 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14645996 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 109. )
GCATTCCAAATCTCATGAGCAGTTCGAAAGTGCGCAACACGATCATAATCCGAACGATAAATACCACTCAAAAGAATGTTGCGAGCTTTACAATTTTGTT[C/T]
AAAAGCAGTTTTTTCAGCAGCAGTATTAATAGCTTCAGGAATCACATAATGATGAGAAACTTTTCTCCAAATATTATAATCTTCAGCCATAATGTAAGAT
ATCTTACATTATGGCTGAAGATTATAATATTTGGAGAAAAGTTTCTCATCATTATGTGATTCCTGAAGCTATTAATACTGCTGCTGAAAAAACTGCTTTT[G/A]
AACAAAATTGTAAAGCTCGCAACATTCTTTTGAGTGGTATTTATCGTTCGGATTATGATCGTGTTGCGCACTTTCGAACTGCTCATGAGATTTGGAATGC
| 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 | 79.00% | 15.40% | 2.22% | 3.34% | NA |
| All Indica | 2759 | 75.10% | 15.70% | 3.70% | 5.55% | NA |
| All Japonica | 1512 | 99.40% | 0.40% | 0.00% | 0.20% | NA |
| Aus | 269 | 23.40% | 76.20% | 0.37% | 0.00% | NA |
| Indica I | 595 | 64.90% | 22.00% | 4.71% | 8.40% | NA |
| Indica II | 465 | 87.50% | 1.70% | 5.81% | 4.95% | NA |
| Indica III | 913 | 79.30% | 15.30% | 1.97% | 3.40% | NA |
| Indica Intermediate | 786 | 70.50% | 19.60% | 3.69% | 6.23% | NA |
| Temperate Japonica | 767 | 99.60% | 0.10% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.70% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 27.10% | 69.80% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 78.90% | 20.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214645996 | C -> DEL | LOC_Os12g25380.1 | N | frameshift_variant | Average:19.643; most accessible tissue: Minghui63 flag leaf, score: 27.515 | N | N | N | N |
| vg1214645996 | C -> T | LOC_Os12g25380.1 | missense_variant ; p.Glu61Lys; MODERATE | nonsynonymous_codon ; E61K | Average:19.643; most accessible tissue: Minghui63 flag leaf, score: 27.515 | unknown | unknown | DELETERIOUS | 0.01 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214645996 | 8.25E-07 | NA | mr1540 | 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 |
| vg1214645996 | 5.06E-06 | 5.06E-06 | mr1540 | 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 |
| vg1214645996 | NA | 6.56E-07 | mr1792 | 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 |
| vg1214645996 | NA | 3.28E-07 | mr1803 | 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 |
| vg1214645996 | NA | 9.97E-06 | mr1456_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 |