Variant ID: vg0514396497 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 14396497 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.05, others allele: 0.00, population size: 241. )
GATTTTAACAGCATCGGGTCACATCATTGTGAGCACATATTGCCAAAGCAAAACGCGCCTAAGTCCCTAGGGATCAACGGGCCACGCTGGTAATAATATT[G/A]
GGCTAAAGTACTGTACAGGCCTAGGCCCATTAGCACTCCCGATACCCTAACAAAACACAGAAGTCCAAGCGACACTTCGTCTTCCCCGCCGAAACTCTCG
CGAGAGTTTCGGCGGGGAAGACGAAGTGTCGCTTGGACTTCTGTGTTTTGTTAGGGTATCGGGAGTGCTAATGGGCCTAGGCCTGTACAGTACTTTAGCC[C/T]
AATATTATTACCAGCGTGGCCCGTTGATCCCTAGGGACTTAGGCGCGTTTTGCTTTGGCAATATGTGCTCACAATGATGTGACCCGATGCTGTTAAAATC
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 | 89.30% | 10.60% | 0.06% | 0.00% | NA |
All Indica | 2759 | 90.30% | 9.60% | 0.11% | 0.00% | NA |
All Japonica | 1512 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
Aus | 269 | 20.10% | 79.90% | 0.00% | 0.00% | NA |
Indica I | 595 | 88.20% | 11.40% | 0.34% | 0.00% | NA |
Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 85.00% | 14.90% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 92.40% | 7.60% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 97.80% | 2.20% | 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 | 94.40% | 5.60% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0514396497 | G -> A | LOC_Os05g24840.1 | upstream_gene_variant ; 275.0bp to feature; MODIFIER | silent_mutation | Average:51.84; most accessible tissue: Minghui63 flag leaf, score: 69.182 | N | N | N | N |
vg0514396497 | G -> A | LOC_Os05g24850.1 | downstream_gene_variant ; 3262.0bp to feature; MODIFIER | silent_mutation | Average:51.84; most accessible tissue: Minghui63 flag leaf, score: 69.182 | N | N | N | N |
vg0514396497 | G -> A | LOC_Os05g24820-LOC_Os05g24840 | intergenic_region ; MODIFIER | silent_mutation | Average:51.84; most accessible tissue: Minghui63 flag leaf, score: 69.182 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0514396497 | NA | 6.88E-09 | mr1608 | 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 |
vg0514396497 | NA | 1.20E-11 | mr1897 | 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 |
vg0514396497 | 1.01E-06 | NA | mr1973_2 | 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 |