| Variant ID: vg1219598626 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 19598626 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )
CGTCAGTATTTTTCTTGGCTAAATATGAAGGAATCAAGCAAAATAAATCAAGTGAACTTGGTTACAATGATCAAAATGTAGATATCTCTTTCAACATTAG[T/C]
TGTCCCATTGGCAAGATTTATTCTCTTATGTCAGTTTCTTGACTATCAACGCTATTGCCTACTATAGTATTTGCTGTTTTCTGGATTTACTTGTGCGATT
AATCGCACAAGTAAATCCAGAAAACAGCAAATACTATAGTAGGCAATAGCGTTGATAGTCAAGAAACTGACATAAGAGAATAAATCTTGCCAATGGGACA[A/G]
CTAATGTTGAAAGAGATATCTACATTTTGATCATTGTAACCAAGTTCACTTGATTTATTTTGCTTGATTCCTTCATATTTAGCCAAGAAAAATACTGACG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.80% | 4.70% | 1.44% | 5.08% | NA |
| All Indica | 2759 | 91.10% | 0.00% | 0.36% | 8.52% | NA |
| All Japonica | 1512 | 82.10% | 14.10% | 3.70% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.30% | 0.00% | 0.34% | 1.34% | NA |
| Indica II | 465 | 83.00% | 0.00% | 0.00% | 16.99% | NA |
| Indica III | 913 | 91.00% | 0.00% | 0.11% | 8.87% | NA |
| Indica Intermediate | 786 | 90.60% | 0.00% | 0.89% | 8.52% | NA |
| Temperate Japonica | 767 | 68.30% | 25.40% | 6.26% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 0.60% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 91.70% | 6.20% | 1.66% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 10.00% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1219598626 | T -> C | LOC_Os12g32470.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.627; most accessible tissue: Zhenshan97 young leaf, score: 55.899 | N | N | N | N |
| vg1219598626 | T -> DEL | N | N | silent_mutation | Average:31.627; most accessible tissue: Zhenshan97 young leaf, score: 55.899 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1219598626 | 3.13E-07 | NA | mr1300 | 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 |
| vg1219598626 | 7.16E-07 | NA | mr1926 | 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 |