| Variant ID: vg1118481523 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 18481523 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )
CGACTCCCGGTCCATCACCACAAATACTCTCCCAAGACATCGAGTCACTTACATATGGAACAAACAAAGAAACTATATTCCGAGACCAAGCTATCTCCAA[C/T]
TTGACTCATTAGCAACAAACAATAGTATTACATACGTATAGTATCCATCTAGAAGTTATAATCATGAAATAAACTCGGATATCCAAATAAACAACCCGAA
TTCGGGTTGTTTATTTGGATATCCGAGTTTATTTCATGATTATAACTTCTAGATGGATACTATACGTATGTAATACTATTGTTTGTTGCTAATGAGTCAA[G/A]
TTGGAGATAGCTTGGTCTCGGAATATAGTTTCTTTGTTTGTTCCATATGTAAGTGACTCGATGTCTTGGGAGAGTATTTGTGGTGATGGACCGGGAGTCG
| 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 | 91.50% | 7.10% | 1.42% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.10% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 74.30% | 21.60% | 4.03% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.20% | 0.50% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 56.20% | 37.20% | 6.65% | 0.00% | NA |
| Tropical Japonica | 504 | 97.20% | 1.60% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 84.20% | 14.10% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1118481523 | C -> T | LOC_Os11g31620.1 | downstream_gene_variant ; 3785.0bp to feature; MODIFIER | silent_mutation | Average:54.03; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg1118481523 | C -> T | LOC_Os11g31610-LOC_Os11g31620 | intergenic_region ; MODIFIER | silent_mutation | Average:54.03; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1118481523 | NA | 5.26E-12 | Plant_height | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg1118481523 | NA | 9.96E-08 | mr1010 | 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 |
| vg1118481523 | NA | 9.09E-08 | mr1163 | 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 |
| vg1118481523 | NA | 8.15E-07 | mr1482 | 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 |
| vg1118481523 | NA | 1.45E-08 | mr1576_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 |
| vg1118481523 | NA | 4.94E-06 | mr1768_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 |
| vg1118481523 | NA | 1.41E-06 | mr1977_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 |