Variant ID: vg1207394291 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 7394291 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 126. )
TTGCTTACATTTGTAATAGTTTTAGTAATTTTGGAATGAACGTGCAGCTTGGAATGTATAATGTTTTTTGGTTTGAAATGCCAAATATATATGTATATTG[G/C]
TTTATTAAAAAAACTTCAATTCCATTTGCACACTCTAGATATTTGCGACGCTTCAGTTATGTATAATTTTAGCCTTGCGCGAATCTTTTTGATAGATTGC
GCAATCTATCAAAAAGATTCGCGCAAGGCTAAAATTATACATAACTGAAGCGTCGCAAATATCTAGAGTGTGCAAATGGAATTGAAGTTTTTTTAATAAA[C/G]
CAATATACATATATATTTGGCATTTCAAACCAAAAAACATTATACATTCCAAGCTGCACGTTCATTCCAAAATTACTAAAACTATTACAAATGTAAGCAA
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 87.90% | 12.00% | 0.08% | 0.00% | NA |
All Indica | 2759 | 87.40% | 12.60% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Aus | 269 | 45.00% | 54.30% | 0.74% | 0.00% | NA |
Indica I | 595 | 89.20% | 10.80% | 0.00% | 0.00% | NA |
Indica II | 465 | 91.00% | 9.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 88.20% | 11.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 82.80% | 16.90% | 0.25% | 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 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 34.40% | 65.60% | 0.00% | 0.00% | NA |
Intermediate | 90 | 88.90% | 11.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1207394291 | G -> C | LOC_Os12g13290.1 | downstream_gene_variant ; 440.0bp to feature; MODIFIER | silent_mutation | Average:18.891; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
vg1207394291 | G -> C | LOC_Os12g13290-LOC_Os12g13295 | intergenic_region ; MODIFIER | silent_mutation | Average:18.891; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1207394291 | 4.06E-06 | NA | mr1032 | 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 |
vg1207394291 | 5.45E-06 | NA | mr1165 | 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 |
vg1207394291 | 3.02E-06 | 1.98E-06 | mr1590 | 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 |
vg1207394291 | NA | 1.44E-06 | mr1808 | 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 |
vg1207394291 | NA | 6.51E-08 | mr1815 | 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 |