| Variant ID: vg1215389587 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 15389587 |
| 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, A: 0.01, others allele: 0.00, population size: 92. )
GTTGATCGAATAAATCGTCAATCCGTGGCAACGGGTACTTGTTCTTTATAGTTACTTCATTTAGGGCTCTATAGTCGATTACCATTCTCTCAGAGCCATC[C/T]
TTTTTCTTAACCAGAAGCACTGGGGCTCCCCAAGTGGATGAGCTAGGTCGCACATAACCTTTACTTTCCAGCTCTTCGATTTGTCTCTTAACTTCTGCTA
TAGCAGAAGTTAAGAGACAAATCGAAGAGCTGGAAAGTAAAGGTTATGTGCGACCTAGCTCATCCACTTGGGGAGCCCCAGTGCTTCTGGTTAAGAAAAA[G/A]
GATGGCTCTGAGAGAATGGTAATCGACTATAGAGCCCTAAATGAAGTAACTATAAAGAACAAGTACCCGTTGCCACGGATTGACGATTTATTCGATCAAC
| 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 | 23.00% | 1.00% | 30.07% | 45.90% | NA |
| All Indica | 2759 | 4.10% | 0.80% | 23.27% | 71.87% | NA |
| All Japonica | 1512 | 60.30% | 1.30% | 33.66% | 4.83% | NA |
| Aus | 269 | 9.30% | 0.70% | 61.71% | 28.25% | NA |
| Indica I | 595 | 3.20% | 0.00% | 11.93% | 84.87% | NA |
| Indica II | 465 | 4.50% | 1.50% | 23.87% | 70.11% | NA |
| Indica III | 913 | 2.60% | 0.80% | 22.34% | 74.26% | NA |
| Indica Intermediate | 786 | 6.10% | 1.00% | 32.57% | 60.31% | NA |
| Temperate Japonica | 767 | 91.50% | 0.10% | 5.74% | 2.61% | NA |
| Tropical Japonica | 504 | 11.90% | 3.40% | 76.98% | 7.74% | NA |
| Japonica Intermediate | 241 | 61.80% | 0.40% | 31.95% | 5.81% | NA |
| VI/Aromatic | 96 | 13.50% | 5.20% | 68.75% | 12.50% | NA |
| Intermediate | 90 | 28.90% | 1.10% | 42.22% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1215389587 | C -> DEL | LOC_Os12g26340.1 | N | frameshift_variant | Average:7.617; most accessible tissue: Callus, score: 16.82 | N | N | N | N |
| vg1215389587 | C -> T | LOC_Os12g26340.1 | synonymous_variant ; p.Lys833Lys; LOW | synonymous_codon | Average:7.617; most accessible tissue: Callus, score: 16.82 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1215389587 | 9.49E-06 | 9.49E-06 | mr1036_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 |
| vg1215389587 | 6.40E-06 | NA | mr1040_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 |
| vg1215389587 | NA | 6.94E-07 | mr1696_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 |
| vg1215389587 | NA | 6.60E-08 | mr1696_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 |
| vg1215389587 | NA | 6.69E-07 | mr1698_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 |
| vg1215389587 | 3.80E-06 | 3.80E-06 | mr1909_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 |