Variant ID: vg0131923446 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 31923446 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 313. )
CCTAGGGCTGCTTGGGTTGAGCCCTAGGCTTGCCTCCATAATCATGCTTAAATTCTCTTAATTCACCATGTAATTTTTCGAGGAAAATACTCCATTAGTT[G/A]
AGCCCTACTTAGCCTTTGGCTTTGATAATTTCTTGCTCCGCCAACTGCAAAAAACGTTTTGGGAAGTAGTTTGAGAGAGTGATGTTTAGTCAGACAAACA
TGTTTGTCTGACTAAACATCACTCTCTCAAACTACTTCCCAAAACGTTTTTTGCAGTTGGCGGAGCAAGAAATTATCAAAGCCAAAGGCTAAGTAGGGCT[C/T]
AACTAATGGAGTATTTTCCTCGAAAAATTACATGGTGAATTAAGAGAATTTAAGCATGATTATGGAGGCAAGCCTAGGGCTCAACCCAAGCAGCCCTAGG
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 | 98.50% | 1.40% | 0.17% | 0.00% | NA |
All Indica | 2759 | 97.40% | 2.30% | 0.29% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 88.60% | 10.10% | 1.34% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0131923446 | G -> A | LOC_Os01g55420.1 | upstream_gene_variant ; 2420.0bp to feature; MODIFIER | silent_mutation | Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 | N | N | N | N |
vg0131923446 | G -> A | LOC_Os01g55410.1 | downstream_gene_variant ; 1040.0bp to feature; MODIFIER | silent_mutation | Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 | N | N | N | N |
vg0131923446 | G -> A | LOC_Os01g55430.1 | downstream_gene_variant ; 3688.0bp to feature; MODIFIER | silent_mutation | Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 | N | N | N | N |
vg0131923446 | G -> A | LOC_Os01g55430.2 | downstream_gene_variant ; 3690.0bp to feature; MODIFIER | silent_mutation | Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 | N | N | N | N |
vg0131923446 | G -> A | LOC_Os01g55410-LOC_Os01g55420 | intergenic_region ; MODIFIER | silent_mutation | Average:69.198; most accessible tissue: Minghui63 panicle, score: 77.956 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0131923446 | 3.78E-06 | 3.78E-06 | mr1469 | 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 |
vg0131923446 | NA | 4.60E-07 | mr1728 | 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 |
vg0131923446 | NA | 3.76E-06 | mr1798 | 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 |
vg0131923446 | NA | 5.09E-06 | mr1860 | 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 |
vg0131923446 | NA | 1.30E-06 | mr1008_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 |