| Variant ID: vg1105852239 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5852239 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCTTCAACCTCTTCTTCCGCGCCTTCTTCAGCTTCTTCATGTTCGAATTCCACTTCACGTTACTGTCCTTAAGATCGCGTTCATTCTTGCCCATCGAATC[G/A]
GGTTATTCACAATTCAGATCTCCAACAGTACTGACCCTACCGATAGTATAGAAAAACCAAATGTCACTCATCTGATGCAACATTATTAATATTCGGAACA
TGTTCCGAATATTAATAATGTTGCATCAGATGAGTGACATTTGGTTTTTCTATACTATCGGTAGGGTCAGTACTGTTGGAGATCTGAATTGTGAATAACC[C/T]
GATTCGATGGGCAAGAATGAACGCGATCTTAAGGACAGTAACGTGAAGTGGAATTCGAACATGAAGAAGCTGAAGAAGGCGCGGAAGAAGAGGTTGAAGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.30% | 32.60% | 0.61% | 0.51% | NA |
| All Indica | 2759 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 10.60% | 85.90% | 1.92% | 1.59% | NA |
| Aus | 269 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 7.00% | 88.00% | 2.74% | 2.22% | NA |
| Tropical Japonica | 504 | 13.50% | 85.70% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 15.80% | 79.70% | 1.66% | 2.90% | NA |
| VI/Aromatic | 96 | 9.40% | 90.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 40.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105852239 | G -> A | LOC_Os11g10670.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.091; most accessible tissue: Callus, score: 72.672 | N | N | N | N |
| vg1105852239 | G -> DEL | N | N | silent_mutation | Average:52.091; most accessible tissue: Callus, score: 72.672 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105852239 | NA | 4.50E-18 | mr1116 | 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 |
| vg1105852239 | NA | 1.26E-18 | mr1242 | 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 |
| vg1105852239 | NA | 1.27E-13 | mr1653 | 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 |
| vg1105852239 | NA | 2.13E-23 | mr1917 | 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 |
| vg1105852239 | NA | 7.04E-14 | mr1924 | 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 |
| vg1105852239 | 1.90E-06 | 1.90E-06 | mr1460_2 | Jap_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 |