Variant ID: vg0414315785 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 14315785 |
Reference Allele: G | Alternative Allele: T |
Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAACTATTAGATTGCTTTTCTCTTTATAAAAAAAACTTTAAGCCACCACATGTCATGTCTTAAAGATCCTTAGAATGAGAAAACAACAAATCATAGGTTC[G/T]
CACTTAGATTGTTTACAAAGATTTTCTTTTTAAAAAAACAATGTACCGTCCACTTCCCCTCCCTGTCCAATCATATGCACATAACACTATTGCATTGTGA
TCACAATGCAATAGTGTTATGTGCATATGATTGGACAGGGAGGGGAAGTGGACGGTACATTGTTTTTTTAAAAAGAAAATCTTTGTAAACAATCTAAGTG[C/A]
GAACCTATGATTTGTTGTTTTCTCATTCTAAGGATCTTTAAGACATGACATGTGGTGGCTTAAAGTTTTTTTTATAAAGAGAAAAGCAATCTAATAGTTA
Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 53.30% | 12.90% | 6.60% | 27.19% | NA |
All Indica | 2759 | 54.70% | 18.20% | 6.81% | 20.26% | NA |
All Japonica | 1512 | 43.70% | 4.00% | 6.88% | 45.44% | NA |
Aus | 269 | 95.50% | 2.60% | 1.49% | 0.37% | NA |
Indica I | 595 | 54.30% | 5.40% | 5.04% | 35.29% | NA |
Indica II | 465 | 86.00% | 6.00% | 2.58% | 5.38% | NA |
Indica III | 913 | 36.40% | 35.30% | 10.08% | 18.29% | NA |
Indica Intermediate | 786 | 57.90% | 15.30% | 6.87% | 19.97% | NA |
Temperate Japonica | 767 | 75.50% | 0.40% | 1.56% | 22.56% | NA |
Tropical Japonica | 504 | 3.80% | 5.60% | 12.10% | 78.57% | NA |
Japonica Intermediate | 241 | 26.10% | 12.00% | 12.86% | 48.96% | NA |
VI/Aromatic | 96 | 39.60% | 29.20% | 10.42% | 20.83% | NA |
Intermediate | 90 | 61.10% | 12.20% | 6.67% | 20.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0414315785 | G -> DEL | N | N | silent_mutation | Average:15.554; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
vg0414315785 | G -> T | LOC_Os04g24850.1 | upstream_gene_variant ; 2496.0bp to feature; MODIFIER | silent_mutation | Average:15.554; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
vg0414315785 | G -> T | LOC_Os04g24850-LOC_Os04g24860 | intergenic_region ; MODIFIER | silent_mutation | Average:15.554; most accessible tissue: Zhenshan97 panicle, score: 36.038 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0414315785 | 3.34E-06 | 3.33E-06 | mr1673 | 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 |