| Variant ID: vg1115211082 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15211082 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGCTGCTTTCCGGAAGACGCATATACCATCGGGAGTGGTGTCTCTCAAGAAGAAGGAATTCAGGTCGCTCACTCAAGGGTCTCGCTCTGTTACGGAGTAT[C/T]
TGCACGAGTTCAATCGTCTGGCTCGTTATGCTCCGGAAGATGTGCGCACTGATGAAGAGCGCCAGGAGAAGTTCTTGGAAGGACTTAATGATGAGCTTTC
GAAAGCTCATCATTAAGTCCTTCCAAGAACTTCTCCTGGCGCTCTTCATCAGTGCGCACATCTTCCGGAGCATAACGAGCCAGACGATTGAACTCGTGCA[G/A]
ATACTCCGTAACAGAGCGAGACCCTTGAGTGAGCGACCTGAATTCCTTCTTCTTGAGAGACACCACTCCCGATGGTATATGCGTCTTCCGGAAAGCAGCG
| 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 | 95.60% | 0.50% | 0.70% | 3.26% | NA |
| All Indica | 2759 | 92.90% | 0.70% | 1.16% | 5.29% | NA |
| All Japonica | 1512 | 99.70% | 0.10% | 0.07% | 0.13% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.00% | 0.74% | NA |
| Indica I | 595 | 95.00% | 0.50% | 0.84% | 3.70% | NA |
| Indica II | 465 | 91.20% | 0.60% | 1.72% | 6.45% | NA |
| Indica III | 913 | 93.10% | 0.80% | 0.55% | 5.59% | NA |
| Indica Intermediate | 786 | 92.00% | 0.80% | 1.78% | 5.47% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1115211082 | C -> T | LOC_Os11g26540.1 | synonymous_variant ; p.Leu426Leu; LOW | synonymous_codon | Average:12.757; most accessible tissue: Minghui63 flag leaf, score: 17.373 | N | N | N | N |
| vg1115211082 | C -> DEL | LOC_Os11g26540.1 | N | frameshift_variant | Average:12.757; most accessible tissue: Minghui63 flag leaf, score: 17.373 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1115211082 | 1.05E-06 | 5.18E-07 | mr1821 | 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 |
| vg1115211082 | 7.48E-06 | 7.48E-06 | mr1430_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 |