| Variant ID: vg1213312673 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13312673 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTGATTTTGAAACAGCCTACCACGCCATACTCGGACTACCGGCGTTAGCCAAGTTCATGGCTGTCCCGCACTACACCTACATGATGATGAAGATGCCAGG[T/A]
CCTCAAGGAGTCATATCCCTGCGGAGCGACATCAAGCAAGCCGTCACTTGCGACAAGGAAAGCTGCAAGATGGCTCAGACCCGCGAGATCACGCTCGCCC
GGGCGAGCGTGATCTCGCGGGTCTGAGCCATCTTGCAGCTTTCCTTGTCGCAAGTGACGGCTTGCTTGATGTCGCTCCGCAGGGATATGACTCCTTGAGG[A/T]
CCTGGCATCTTCATCATCATGTAGGTGTAGTGCGGGACAGCCATGAACTTGGCTAACGCCGGTAGTCCGAGTATGGCGTGGTAGGCTGTTTCAAAATCAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.50% | 0.10% | 4.40% | 74.95% | NA |
| All Indica | 2759 | 6.50% | 0.20% | 1.41% | 91.84% | NA |
| All Japonica | 1512 | 48.30% | 0.00% | 1.65% | 50.00% | NA |
| Aus | 269 | 7.40% | 0.40% | 48.33% | 43.87% | NA |
| Indica I | 595 | 12.30% | 0.20% | 0.67% | 86.89% | NA |
| Indica II | 465 | 6.70% | 0.00% | 0.86% | 92.47% | NA |
| Indica III | 913 | 1.20% | 0.20% | 1.75% | 96.82% | NA |
| Indica Intermediate | 786 | 8.30% | 0.40% | 1.91% | 89.44% | NA |
| Temperate Japonica | 767 | 81.90% | 0.00% | 0.13% | 17.99% | NA |
| Tropical Japonica | 504 | 7.10% | 0.00% | 3.17% | 89.68% | NA |
| Japonica Intermediate | 241 | 27.80% | 0.00% | 3.32% | 68.88% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 12.50% | 85.42% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 2.22% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213312673 | T -> DEL | LOC_Os12g23520.1 | N | frameshift_variant | Average:15.559; most accessible tissue: Zhenshan97 root, score: 34.536 | N | N | N | N |
| vg1213312673 | T -> A | LOC_Os12g23520.1 | synonymous_variant ; p.Gly1559Gly; LOW | synonymous_codon | Average:15.559; most accessible tissue: Zhenshan97 root, score: 34.536 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1213312673 | NA | 5.88E-13 | mr1149 | 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 |
| vg1213312673 | NA | 5.46E-20 | mr1588 | 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 |
| vg1213312673 | 1.99E-07 | 2.15E-08 | mr1588 | Ind_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 |
| vg1213312673 | NA | 7.22E-25 | mr1588_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 |
| vg1213312673 | NA | 9.31E-08 | mr1588_2 | 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 |