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Detailed information for vg0604777948:

Variant ID: vg0604777948 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4777948
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCTGACACATCACATTCCTACTCATCATGCAACTTCCATCAGCAGATAAGTTGCAGATAGATCAACCCGTGCATCGAATTATTGAAATCGATCATTGT[G/A]
TGTTGGTATGTATATATGATGAATCTCTCTGAAGTATGTACCTTTTTCCTCCCCTAATGCAAGCTGGTGGTTCCTTTGGTATATATCTTGATTCTTGAGG

Reverse complement sequence

CCTCAAGAATCAAGATATATACCAAAGGAACCACCAGCTTGCATTAGGGGAGGAAAAAGGTACATACTTCAGAGAGATTCATCATATATACATACCAACA[C/T]
ACAATGATCGATTTCAATAATTCGATGCACGGGTTGATCTATCTGCAACTTATCTGCTGATGGAAGTTGCATGATGAGTAGGAATGTGATGTGTCAGGAA

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 77.30% 22.70% 0.00% 0.00% NA
All Indica  2759 66.70% 33.30% 0.00% 0.00% NA
All Japonica  1512 95.00% 5.00% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 55.00% 45.00% 0.00% 0.00% NA
Indica II  465 86.90% 13.10% 0.00% 0.00% NA
Indica III  913 63.60% 36.40% 0.00% 0.00% NA
Indica Intermediate  786 67.00% 33.00% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 90.30% 9.70% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 35.40% 64.60% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 0.00% 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
vg0604777948 G -> A LOC_Os06g09420-LOC_Os06g09430 intergenic_region ; MODIFIER silent_mutation Average:44.061; most accessible tissue: Zhenshan97 flower, score: 74.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604777948 1.91E-06 3.54E-12 mr1201 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
vg0604777948 6.82E-06 6.35E-13 mr1201 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
vg0604777948 NA 6.01E-09 mr1219 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
vg0604777948 NA 4.88E-11 mr1219 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
vg0604777948 NA 9.07E-11 mr1274 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
vg0604777948 NA 6.88E-11 mr1274 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
vg0604777948 NA 1.58E-09 mr1201_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
vg0604777948 NA 7.38E-10 mr1201_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
vg0604777948 NA 2.34E-07 mr1219_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
vg0604777948 NA 1.04E-08 mr1219_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
vg0604777948 NA 3.39E-10 mr1274_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
vg0604777948 NA 1.62E-10 mr1274_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
vg0604777948 NA 9.40E-06 mr1406_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