Variant ID: vg0415467485 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 15467485 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTCTTCCAAGGCATCCCGCGAACCAGTCCTTAATTGCCATGGGCATGACCATCAAAACCATGCACCCACAGCCCACCATTTAATATATTTTAATTAACC[G/A]
ACACCGGAGCGGTGGCATTAACCAACATCATTACTAGAATCTAATATCTATGCATTAATGTAGTCCCCCATTGTGTGCTAGTTGAACTAAGCAAGGCTAA
TTAGCCTTGCTTAGTTCAACTAGCACACAATGGGGGACTACATTAATGCATAGATATTAGATTCTAGTAATGATGTTGGTTAATGCCACCGCTCCGGTGT[C/T]
GGTTAATTAAAATATATTAAATGGTGGGCTGTGGGTGCATGGTTTTGATGGTCATGCCCATGGCAATTAAGGACTGGTTCGCGGGATGCCTTGGAAGAAC
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 81.30% | 0.30% | 1.63% | 16.74% | NA |
All Indica | 2759 | 86.40% | 0.40% | 1.92% | 11.24% | NA |
All Japonica | 1512 | 82.30% | 0.10% | 1.12% | 16.47% | NA |
Aus | 269 | 17.10% | 0.40% | 2.23% | 80.30% | NA |
Indica I | 595 | 94.50% | 0.30% | 0.50% | 4.71% | NA |
Indica II | 465 | 80.60% | 0.60% | 3.01% | 15.70% | NA |
Indica III | 913 | 84.20% | 0.20% | 2.63% | 12.92% | NA |
Indica Intermediate | 786 | 86.30% | 0.60% | 1.53% | 11.58% | NA |
Temperate Japonica | 767 | 67.30% | 0.30% | 2.22% | 30.25% | NA |
Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
Japonica Intermediate | 241 | 95.00% | 0.00% | 0.00% | 4.98% | NA |
VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
Intermediate | 90 | 90.00% | 0.00% | 1.11% | 8.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0415467485 | G -> DEL | N | N | silent_mutation | Average:52.455; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 | N | N | N | N |
vg0415467485 | G -> A | LOC_Os04g26520.1 | upstream_gene_variant ; 719.0bp to feature; MODIFIER | silent_mutation | Average:52.455; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 | N | N | N | N |
vg0415467485 | G -> A | LOC_Os04g26510-LOC_Os04g26520 | intergenic_region ; MODIFIER | silent_mutation | Average:52.455; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0415467485 | 2.97E-06 | 2.98E-06 | mr1562 | 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 |
vg0415467485 | 7.02E-06 | NA | mr1754 | 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 |
vg0415467485 | NA | 7.36E-06 | mr1754 | 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 |