| Variant ID: vg1211535626 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 11535626 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 103. )
TCATGCGCAAATGGATTGCTATGACTTTGTTTCCTAGAGGTGATCTTATACCCATTAGGGGGGATGAATTGTTTGTCATGTTCGCCATGGTTAGAAAAAT[T/C]
AAAATTGCTCCTGTGAAATGTATGATAAGGCAATGGTTAGAAAATATAAAGTTCACTGCACTTCTCTGATTACTCGGATAGCAAAAGGGCTAGGGGTTGT
ACAACCCCTAGCCCTTTTGCTATCCGAGTAATCAGAGAAGTGCAGTGAACTTTATATTTTCTAACCATTGCCTTATCATACATTTCACAGGAGCAATTTT[A/G]
ATTTTTCTAACCATGGCGAACATGACAAACAATTCATCCCCCCTAATGGGTATAAGATCACCTCTAGGAAACAAAGTCATAGCAATCCATTTGCGCATGA
| 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 | 39.20% | 17.10% | 1.59% | 42.13% | NA |
| All Indica | 2759 | 61.10% | 3.70% | 1.85% | 33.38% | NA |
| All Japonica | 1512 | 7.10% | 44.40% | 0.99% | 47.49% | NA |
| Aus | 269 | 5.60% | 3.00% | 2.23% | 89.22% | NA |
| Indica I | 595 | 44.40% | 6.70% | 3.19% | 45.71% | NA |
| Indica II | 465 | 71.00% | 4.50% | 1.29% | 23.23% | NA |
| Indica III | 913 | 67.70% | 0.50% | 0.99% | 30.78% | NA |
| Indica Intermediate | 786 | 60.20% | 4.60% | 2.16% | 33.08% | NA |
| Temperate Japonica | 767 | 9.60% | 76.50% | 0.39% | 13.43% | NA |
| Tropical Japonica | 504 | 4.40% | 5.00% | 1.59% | 89.09% | NA |
| Japonica Intermediate | 241 | 5.00% | 24.50% | 1.66% | 68.88% | NA |
| VI/Aromatic | 96 | 18.80% | 2.10% | 0.00% | 79.17% | NA |
| Intermediate | 90 | 28.90% | 27.80% | 3.33% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1211535626 | T -> C | LOC_Os12g19790.1 | intron_variant ; MODIFIER | silent_mutation | Average:8.172; most accessible tissue: Callus, score: 32.13 | N | N | N | N |
| vg1211535626 | T -> DEL | N | N | silent_mutation | Average:8.172; most accessible tissue: Callus, score: 32.13 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1211535626 | NA | 4.87E-06 | mr1639 | 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 |
| vg1211535626 | NA | 4.16E-06 | mr1874_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 |