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Detailed information for vg1101201264:

Variant ID: vg1101201264 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1201264
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.57, A: 0.43, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAAGGTGCCTAAATCAAACCAAGGTGAATTAGGAGGTGGGGATTTACAACGAATCTTCTAATGAGGGGGCATCTCTCAAACTCAGAGTGATATTTGAG[A/G]
GTGGTTTTTGCAATTTTCCCTTAAAAATAAAACACAGTGTTGCCCATATGACAGGCAGCAAGCTAGCAGTAACCAAATGATATATACGTGTGGCATAAGA

Reverse complement sequence

TCTTATGCCACACGTATATATCATTTGGTTACTGCTAGCTTGCTGCCTGTCATATGGGCAACACTGTGTTTTATTTTTAAGGGAAAATTGCAAAAACCAC[T/C]
CTCAAATATCACTCTGAGTTTGAGAGATGCCCCCTCATTAGAAGATTCGTTGTAAATCCCCACCTCCTAATTCACCTTGGTTTGATTTAGGCACCTTTTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.80% 35.10% 0.06% 0.00% NA
All Indica  2759 95.60% 4.40% 0.00% 0.00% NA
All Japonica  1512 3.10% 96.90% 0.00% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 87.70% 12.30% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 5.60% 0.00% 0.00% NA
Temperate Japonica  767 2.70% 97.30% 0.00% 0.00% NA
Tropical Japonica  504 2.60% 97.40% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 94.60% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 52.20% 44.40% 3.33% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1101201264 A -> G LOC_Os11g03260.1 upstream_gene_variant ; 3433.0bp to feature; MODIFIER silent_mutation Average:37.255; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg1101201264 A -> G LOC_Os11g03270.1 upstream_gene_variant ; 1476.0bp to feature; MODIFIER silent_mutation Average:37.255; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg1101201264 A -> G LOC_Os11g03260-LOC_Os11g03270 intergenic_region ; MODIFIER silent_mutation Average:37.255; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1101201264 NA 2.52E-38 mr1082 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
vg1101201264 NA 4.62E-07 mr1082 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
vg1101201264 NA 3.45E-08 mr1093 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
vg1101201264 NA 1.82E-07 mr1226 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
vg1101201264 NA 7.45E-07 mr1411 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
vg1101201264 NA 3.25E-07 mr1518 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
vg1101201264 NA 3.63E-18 mr1529 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
vg1101201264 NA 9.43E-11 mr1023_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
vg1101201264 NA 3.83E-12 mr1132_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
vg1101201264 NA 1.32E-12 mr1178_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
vg1101201264 6.95E-07 NA mr1380_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
vg1101201264 NA 1.95E-14 mr1529_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
vg1101201264 4.88E-07 NA mr1561_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
vg1101201264 2.60E-07 NA mr1908_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
vg1101201264 3.19E-06 1.88E-06 mr1908_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