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Detailed information for vg0823106771:

Variant ID: vg0823106771 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 23106771
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, G: 0.01, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGCCTACTCCATTCATCCAGGAAGTACGAAGATGTACCAAGATATCAAGGCATACTTCTGGTGGGCTGGAATGAAGCGAGATGTCACAGAATACGTAG[G/C]
CTTGTGTGACATTTGCCAAAGAGTCAAGGCAGAGCATCATTGACCAGCTGGTCTGCTGCAACCCGTACCGATTCCCGAGTGGAAATGGGAAGAGATCGGA

Reverse complement sequence

TCCGATCTCTTCCCATTTCCACTCGGGAATCGGTACGGGTTGCAGCAGACCAGCTGGTCAATGATGCTCTGCCTTGACTCTTTGGCAAATGTCACACAAG[C/G]
CTACGTATTCTGTGACATCTCGCTTCATTCCAGCCCACCAGAAGTATGCCTTGATATCTTGGTACATCTTCGTACTTCCTGGATGAATGGAGTAGGCGGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 17.00% 14.60% 18.54% 49.87% NA
All Indica  2759 1.00% 1.00% 17.25% 80.75% NA
All Japonica  1512 49.20% 42.70% 7.08% 1.06% NA
Aus  269 2.60% 1.10% 76.95% 19.33% NA
Indica I  595 0.50% 0.80% 8.91% 89.75% NA
Indica II  465 1.30% 1.50% 32.47% 64.73% NA
Indica III  913 0.80% 0.40% 11.06% 87.73% NA
Indica Intermediate  786 1.50% 1.40% 21.76% 75.32% NA
Temperate Japonica  767 17.50% 72.40% 8.87% 1.30% NA
Tropical Japonica  504 91.70% 4.40% 3.37% 0.60% NA
Japonica Intermediate  241 61.40% 28.20% 9.13% 1.24% NA
VI/Aromatic  96 6.20% 1.00% 68.75% 23.96% NA
Intermediate  90 22.20% 13.30% 22.22% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0823106771 G -> C LOC_Os08g36620.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:9.143; most accessible tissue: Callus, score: 29.731 N N N N
vg0823106771 G -> DEL N N silent_mutation Average:9.143; most accessible tissue: Callus, score: 29.731 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0823106771 NA 3.35E-23 mr1115 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
vg0823106771 NA 1.58E-07 mr1229 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
vg0823106771 NA 9.16E-09 mr1229 Jap_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
vg0823106771 NA 1.46E-06 mr1252 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
vg0823106771 NA 5.00E-07 mr1763 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
vg0823106771 NA 9.31E-09 mr1880 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
vg0823106771 NA 1.07E-11 mr1880 Jap_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
vg0823106771 NA 1.23E-06 mr1977 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
vg0823106771 5.60E-06 NA mr1181_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
vg0823106771 NA 5.24E-08 mr1952_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
vg0823106771 NA 1.59E-09 mr1952_2 Jap_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