| Variant ID: vg1123041283 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23041283 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.03, others allele: 0.00, population size: 195. )
ATAGAAATTATTTGCCTCTATCCAGCTTTTGCGGCAGCTTTGTATTTCCTAATTTTGATTCGGTGGACCTAAAGGGATTTAGTGCTCAATATTTTTTTTT[C/A]
TTTTGAAATTGACGACGGCAGGAGCTCTGCCGGATATATTGAGAAGTAAAAGTTCAGAAGTACAAAAGGTTCTGGGAAAAGGGAGAATAGAGGAGGTTAC
GTAACCTCCTCTATTCTCCCTTTTCCCAGAACCTTTTGTACTTCTGAACTTTTACTTCTCAATATATCCGGCAGAGCTCCTGCCGTCGTCAATTTCAAAA[G/T]
AAAAAAAAATATTGAGCACTAAATCCCTTTAGGTCCACCGAATCAAAATTAGGAAATACAAAGCTGCCGCAAAAGCTGGATAGAGGCAAATAATTTCTAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.00% | 24.10% | 0.04% | 1.86% | NA |
| All Indica | 2759 | 63.70% | 35.90% | 0.04% | 0.36% | NA |
| All Japonica | 1512 | 93.80% | 5.50% | 0.00% | 0.66% | NA |
| Aus | 269 | 68.00% | 9.30% | 0.37% | 22.30% | NA |
| Indica I | 595 | 66.70% | 33.10% | 0.00% | 0.17% | NA |
| Indica II | 465 | 64.10% | 35.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 70.40% | 28.70% | 0.00% | 0.88% | NA |
| Indica Intermediate | 786 | 53.30% | 46.40% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 96.20% | 2.90% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 95.80% | 4.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 82.20% | 17.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 79.20% | 15.60% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 70.00% | 26.70% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123041283 | C -> A | LOC_Os11g38760-LOC_Os11g38765 | intergenic_region ; MODIFIER | silent_mutation | Average:34.237; most accessible tissue: Callus, score: 58.006 | N | N | N | N |
| vg1123041283 | C -> DEL | N | N | silent_mutation | Average:34.237; most accessible tissue: Callus, score: 58.006 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1123041283 | NA | 3.71E-06 | mr1157 | 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 |
| vg1123041283 | 1.84E-06 | 1.15E-07 | mr1446 | 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 |