| Variant ID: vg1111250824 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 11250824 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCGAACTCCCTCCGTCGACCAGTATTCGTCGGACCTCGAAACCAGCTATCTCTGCTGAGATTACCAAAGGATCTTGATGCGAGAACATAACTCCTTCTGC[G/A]
TCTTCCGGCCCAAAAGAAATTAGCTGGTTCAGATATTGCGGCGCCCCTTCGCCCATCGAAGTGATGCTGTGGACCATACGGGTCTGCATCTTCTTTTGCC
GGCAAAAGAAGATGCAGACCCGTATGGTCCACAGCATCACTTCGATGGGCGAAGGGGCGCCGCAATATCTGAACCAGCTAATTTCTTTTGGGCCGGAAGA[C/T]
GCAGAAGGAGTTATGTTCTCGCATCAAGATCCTTTGGTAATCTCAGCAGAGATAGCTGGTTTCGAGGTCCGACGAATACTGGTCGACGGAGGGAGTTCGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.30% | 6.90% | 4.32% | 5.50% | NA |
| All Indica | 2759 | 73.60% | 11.40% | 6.02% | 8.92% | NA |
| All Japonica | 1512 | 98.50% | 0.30% | 0.93% | 0.33% | NA |
| Aus | 269 | 89.60% | 1.50% | 8.18% | 0.74% | NA |
| Indica I | 595 | 69.90% | 12.90% | 7.39% | 9.75% | NA |
| Indica II | 465 | 92.70% | 0.00% | 3.44% | 3.87% | NA |
| Indica III | 913 | 65.80% | 18.00% | 5.26% | 10.95% | NA |
| Indica Intermediate | 786 | 74.30% | 9.40% | 7.38% | 8.91% | NA |
| Temperate Japonica | 767 | 99.30% | 0.10% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 98.60% | 0.60% | 0.60% | 0.20% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 4.15% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 4.40% | 2.22% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1111250824 | G -> A | LOC_Os11g19520.1 | synonymous_variant ; p.Asp589Asp; LOW | synonymous_codon | Average:48.312; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg1111250824 | G -> DEL | LOC_Os11g19520.1 | N | frameshift_variant | Average:48.312; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1111250824 | NA | 7.92E-08 | mr1627 | 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 |
| vg1111250824 | NA | 1.27E-06 | mr1031_2 | 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 |
| vg1111250824 | NA | 2.72E-09 | mr1627_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 |