Variant ID: vg0301975407 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 1975407 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 130. )
AGCACTTATGGCTAATCATGGACTAATTAGGCTCAAAAGATTCGTCTCGCGATATCCATGCAAACTGTGCAATTAGTTTTTGTTTTTATCTATATTTAAT[G/A]
CTCCATGCATGTATCCAAAGATTTGATGTGACGTTTTTGGGGGAAAAAAATTTTGAGAACTAAACCAAGCCTGAATAGATTCATACGGTTTTGTTGAAAA
TTTTCAACAAAACCGTATGAATCTATTCAGGCTTGGTTTAGTTCTCAAAATTTTTTTCCCCCAAAAACGTCACATCAAATCTTTGGATACATGCATGGAG[C/T]
ATTAAATATAGATAAAAACAAAAACTAATTGCACAGTTTGCATGGATATCGCGAGACGAATCTTTTGAGCCTAATTAGTCCATGATTAGCCATAAGTGCT
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 | 95.00% | 5.00% | 0.04% | 0.00% | NA |
All Indica | 2759 | 91.50% | 8.40% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 73.40% | 26.60% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.70% | 0.10% | 0.22% | 0.00% | NA |
Indica Intermediate | 786 | 90.70% | 9.30% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 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 | 98.90% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0301975407 | G -> A | LOC_Os03g04300.3 | downstream_gene_variant ; 780.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0301975407 | G -> A | LOC_Os03g04300.2 | downstream_gene_variant ; 804.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0301975407 | G -> A | LOC_Os03g04300.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0301975407 | NA | 5.26E-06 | mr1533 | 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 |
vg0301975407 | NA | 4.54E-06 | mr1980 | 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 |
vg0301975407 | 6.07E-06 | 1.10E-08 | mr1533_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 |