| Variant ID: vg1124410475 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24410475 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, C: 0.16, others allele: 0.00, population size: 62. )
AGTTTATTTTTTTTAAAAAAAGACATGCATGAAAATTTGATCAGTTAATTTTTGCCATGTTTGATGTGGCTCAGATCCACTTACTTCGTGCCACACCCAT[T/C]
ATCTCCATCAGTCATCCCCAAATCCAACCAGAGCTCGAGCTCGCCACGGATGACCCACCACCACCACCCATGCACGCATGGATGACGACAAGCTCGCCCT
AGGGCGAGCTTGTCGTCATCCATGCGTGCATGGGTGGTGGTGGTGGGTCATCCGTGGCGAGCTCGAGCTCTGGTTGGATTTGGGGATGACTGATGGAGAT[A/G]
ATGGGTGTGGCACGAAGTAAGTGGATCTGAGCCACATCAAACATGGCAAAAATTAACTGATCAAATTTTCATGCATGTCTTTTTTTAAAAAAAATAAACT
| 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 | 47.60% | 23.80% | 9.59% | 19.04% | NA |
| All Indica | 2759 | 58.30% | 10.40% | 11.78% | 19.46% | NA |
| All Japonica | 1512 | 35.50% | 43.90% | 3.51% | 17.06% | NA |
| Aus | 269 | 16.70% | 44.60% | 20.45% | 18.22% | NA |
| Indica I | 595 | 71.90% | 7.60% | 10.59% | 9.92% | NA |
| Indica II | 465 | 54.40% | 11.20% | 14.62% | 19.78% | NA |
| Indica III | 913 | 55.80% | 11.10% | 8.11% | 25.08% | NA |
| Indica Intermediate | 786 | 53.30% | 11.50% | 15.27% | 19.97% | NA |
| Temperate Japonica | 767 | 62.60% | 20.30% | 4.56% | 12.52% | NA |
| Tropical Japonica | 504 | 4.00% | 68.30% | 1.98% | 25.79% | NA |
| Japonica Intermediate | 241 | 15.40% | 68.00% | 3.32% | 13.28% | NA |
| VI/Aromatic | 96 | 14.60% | 26.00% | 12.50% | 46.88% | NA |
| Intermediate | 90 | 50.00% | 28.90% | 8.89% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1124410475 | T -> DEL | N | N | silent_mutation | Average:32.439; most accessible tissue: Callus, score: 54.002 | N | N | N | N |
| vg1124410475 | T -> C | LOC_Os11g40800.1 | upstream_gene_variant ; 4173.0bp to feature; MODIFIER | silent_mutation | Average:32.439; most accessible tissue: Callus, score: 54.002 | N | N | N | N |
| vg1124410475 | T -> C | LOC_Os11g40790-LOC_Os11g40800 | intergenic_region ; MODIFIER | silent_mutation | Average:32.439; most accessible tissue: Callus, score: 54.002 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124410475 | NA | 1.19E-06 | mr1309 | 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 |
| vg1124410475 | 3.30E-06 | NA | mr1238_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 |
| vg1124410475 | NA | 7.71E-07 | mr1398_2 | Jap_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 |
| vg1124410475 | NA | 1.11E-06 | mr1566_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 |
| vg1124410475 | 4.69E-07 | NA | mr1609_2 | 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 |
| vg1124410475 | NA | 1.56E-08 | mr1609_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 |
| vg1124410475 | NA | 2.12E-07 | mr1696_2 | Jap_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 |
| vg1124410475 | 1.72E-06 | NA | mr1841_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 |
| vg1124410475 | 6.28E-07 | NA | mr1900_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 |
| vg1124410475 | NA | 2.36E-06 | mr1959_2 | Jap_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 |
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