Variant ID: vg0415345317 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 15345317 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGAATATGAAGGGATACAAAGGACGGGCAGGGTTATCACCACCTGTCGTCTACCCTACTTTCCGTGTAGCACACAACAAACGAAGGTAACCTCTAACCTA[G/A]
ACACCACACCTACGTTATCGATTACTACTCTAGCCTCGGCCAAGAACTATCTTGTTTATCCAGAGTCTTAGTACTAGAGCATTAAGTATAAATACTAAGC
GCTTAGTATTTATACTTAATGCTCTAGTACTAAGACTCTGGATAAACAAGATAGTTCTTGGCCGAGGCTAGAGTAGTAATCGATAACGTAGGTGTGGTGT[C/T]
TAGGTTAGAGGTTACCTTCGTTTGTTGTGTGCTACACGGAAAGTAGGGTAGACGACAGGTGGTGATAACCCTGCCCGTCCTTTGTATCCCTTCATATTCG
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 | 73.30% | 1.90% | 13.92% | 10.92% | NA |
All Indica | 2759 | 75.00% | 3.10% | 16.75% | 5.18% | NA |
All Japonica | 1512 | 79.30% | 0.10% | 0.79% | 19.84% | NA |
Aus | 269 | 13.40% | 0.00% | 63.57% | 23.05% | NA |
Indica I | 595 | 91.40% | 0.00% | 8.24% | 0.34% | NA |
Indica II | 465 | 67.30% | 14.80% | 16.13% | 1.72% | NA |
Indica III | 913 | 64.60% | 0.80% | 24.75% | 9.86% | NA |
Indica Intermediate | 786 | 79.10% | 1.10% | 14.25% | 5.47% | NA |
Temperate Japonica | 767 | 61.70% | 0.00% | 1.04% | 37.29% | NA |
Tropical Japonica | 504 | 99.00% | 0.00% | 0.40% | 0.60% | NA |
Japonica Intermediate | 241 | 94.20% | 0.40% | 0.83% | 4.56% | NA |
VI/Aromatic | 96 | 91.70% | 0.00% | 5.21% | 3.12% | NA |
Intermediate | 90 | 80.00% | 2.20% | 8.89% | 8.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0415345317 | G -> DEL | N | N | silent_mutation | Average:48.062; most accessible tissue: Minghui63 young leaf, score: 68.745 | N | N | N | N |
vg0415345317 | G -> A | LOC_Os04g26310.1 | downstream_gene_variant ; 3243.0bp to feature; MODIFIER | silent_mutation | Average:48.062; most accessible tissue: Minghui63 young leaf, score: 68.745 | N | N | N | N |
vg0415345317 | G -> A | LOC_Os04g26320.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.062; most accessible tissue: Minghui63 young leaf, score: 68.745 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0415345317 | 3.97E-08 | NA | mr1071_2 | 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 |
vg0415345317 | 7.51E-07 | NA | mr1080_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 |
vg0415345317 | 1.39E-06 | NA | mr1203_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 |
vg0415345317 | NA | 1.16E-06 | mr1362_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 |