Variant ID: vg0404350615 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 4350615 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.01, others allele: 0.00, population size: 72. )
TCCTGTAACTGACTTCTCTTCTATCATATTTTGCCCTGCTACTTGAAATAAAAATCAGGTACATCCCTTCTTTATGTATAAAATTTCTTTCATTGTAGGT[G/C]
AAAATTTATTTGATTTTAGAATCTTTCTCCTGATTATATGAGACTGTGGTGCTAGATTTTATAACCTGTGAAGATCACAACTGAAAGGCTGAAAGCAATG
CATTGCTTTCAGCCTTTCAGTTGTGATCTTCACAGGTTATAAAATCTAGCACCACAGTCTCATATAATCAGGAGAAAGATTCTAAAATCAAATAAATTTT[C/G]
ACCTACAATGAAAGAAATTTTATACATAAAGAAGGGATGTACCTGATTTTTATTTCAAGTAGCAGGGCAAAATATGATAGAAGAGAAGTCAGTTACAGGA
Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 61.80% | 38.10% | 0.06% | 0.00% | NA |
All Indica | 2759 | 89.10% | 10.90% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 10.30% | 89.70% | 0.00% | 0.00% | NA |
Aus | 269 | 77.30% | 22.30% | 0.37% | 0.00% | NA |
Indica I | 595 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
Indica II | 465 | 86.50% | 13.50% | 0.00% | 0.00% | NA |
Indica III | 913 | 93.40% | 6.50% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 82.60% | 17.30% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 5.20% | 94.80% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 9.10% | 90.90% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 28.60% | 71.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 53.10% | 46.90% | 0.00% | 0.00% | NA |
Intermediate | 90 | 57.80% | 42.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0404350615 | G -> C | LOC_Os04g08190.1 | upstream_gene_variant ; 2525.0bp to feature; MODIFIER | silent_mutation | Average:38.127; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
vg0404350615 | G -> C | LOC_Os04g08170.1 | downstream_gene_variant ; 4402.0bp to feature; MODIFIER | silent_mutation | Average:38.127; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
vg0404350615 | G -> C | LOC_Os04g08180.1 | intron_variant ; MODIFIER | silent_mutation | Average:38.127; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0404350615 | NA | 2.94E-16 | mr1035 | 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 |
vg0404350615 | NA | 6.92E-14 | mr1626 | 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 |
vg0404350615 | NA | 1.61E-09 | mr1637 | 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 |
vg0404350615 | NA | 7.79E-14 | mr1035_2 | 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 |
vg0404350615 | 3.21E-06 | 3.21E-06 | mr1035_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 |