| Variant ID: vg1125862812 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25862812 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTACAACTCAGTCAACTTTTCGGCTCCATGAAGCAGCTATGGAACCAATCAATTTATTCATAGTAGATGACGCAGCCAAAATCAATGAGTGTGATCTCAT[T/C]
ATTCCATTGCGCCTGCCAGTGACACACATTTTGATGCTAGGCGACGACTTCAATTTGCAGCCAAGCAAGGTAATCTTTTCTTTCTGATTTTCTAGTGTAT
ATACACTAGAAAATCAGAAAGAAAAGATTACCTTGCTTGGCTGCAAATTGAAGTCGTCGCCTAGCATCAAAATGTGTGTCACTGGCAGGCGCAATGGAAT[A/G]
ATGAGATCACACTCATTGATTTTGGCTGCGTCATCTACTATGAATAAATTGATTGGTTCCATAGCTGCTTCATGGAGCCGAAAAGTTGACTGAGTTGTAG
| 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 | 95.10% | 0.80% | 1.69% | 2.41% | NA |
| All Indica | 2759 | 95.50% | 1.40% | 2.86% | 0.22% | NA |
| All Japonica | 1512 | 93.50% | 0.00% | 0.07% | 6.48% | NA |
| Aus | 269 | 98.50% | 0.00% | 0.00% | 1.49% | NA |
| Indica I | 595 | 81.70% | 6.60% | 11.60% | 0.17% | NA |
| Indica II | 465 | 98.10% | 0.00% | 1.94% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 99.50% | 0.00% | 0.13% | 0.38% | NA |
| Temperate Japonica | 767 | 87.50% | 0.00% | 0.13% | 12.39% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125862812 | T -> DEL | LOC_Os11g42910.1 | N | frameshift_variant | Average:26.668; most accessible tissue: Callus, score: 45.563 | N | N | N | N |
| vg1125862812 | T -> C | LOC_Os11g42910.1 | synonymous_variant ; p.Ile753Ile; LOW | synonymous_codon | Average:26.668; most accessible tissue: Callus, score: 45.563 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125862812 | 8.00E-10 | 1.07E-10 | mr1191 | 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 |
| vg1125862812 | 8.64E-10 | 8.71E-11 | mr1644 | 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 |
| vg1125862812 | 3.23E-12 | 6.58E-15 | mr1191_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 |