Variant ID: vg1215800897 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 15800897 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAAGACGGCCGACCTAGTGCCTAGGCGGAAGCCACCAAGAACTACATACGTCACAGCGGTTGGGTTGTGTGGGATAACGTGCCTGTCAGTACGGTGTACT[G/A]
GCGCAGAACAAGGGCACACGGAGATCATGAGAGCTTTGTCCCATATTCGGAGAAAGAGATGTTGTGGACCACAATGCTCGAGACATTCACCCTTCCCACA
TGTGGGAAGGGTGAATGTCTCGAGCATTGTGGTCCACAACATCTCTTTCTCCGAATATGGGACAAAGCTCTCATGATCTCCGTGTGCCCTTGTTCTGCGC[C/T]
AGTACACCGTACTGACAGGCACGTTATCCCACACAACCCAACCGCTGTGACGTATGTAGTTCTTGGTGGCTTCCGCCTAGGCACTAGGTCGGCCGTCTTC
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 | 84.60% | 15.30% | 0.06% | 0.00% | NA |
All Indica | 2759 | 74.20% | 25.70% | 0.11% | 0.00% | NA |
All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Indica I | 595 | 87.90% | 12.10% | 0.00% | 0.00% | NA |
Indica II | 465 | 93.80% | 6.00% | 0.22% | 0.00% | NA |
Indica III | 913 | 51.90% | 48.00% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 78.00% | 21.90% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 93.30% | 6.70% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1215800897 | G -> A | LOC_Os12g26980.1 | upstream_gene_variant ; 3889.0bp to feature; MODIFIER | silent_mutation | Average:39.572; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | N | N | N | N |
vg1215800897 | G -> A | LOC_Os12g26970.1 | downstream_gene_variant ; 2704.0bp to feature; MODIFIER | silent_mutation | Average:39.572; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | N | N | N | N |
vg1215800897 | G -> A | LOC_Os12g26970-LOC_Os12g26980 | intergenic_region ; MODIFIER | silent_mutation | Average:39.572; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1215800897 | 1.26E-06 | NA | mr1438 | 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 |
vg1215800897 | 6.54E-06 | NA | mr1438 | 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 |