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Detailed information for vg0405797011:

Variant ID: vg0405797011 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5797011
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.55, T: 0.44, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCACTGATCGGTGCTTGATGAGGACATTAGTGCCGGCTTTAGTCGTTGTTGGCACCAAGGTAACGTGTGTTGCGGTCGTAGGGTGCTGGTGATGAAGA[A/T]
CACAGTACGGCGGCGGCGATGGGAATTGCCAAGATGGAGTTTGCCCTTCGATTCCCCTTAGCGCTCCTTAGGATCAGTAGAACTTAGGGTTTAGGATATC

Reverse complement sequence

GATATCCTAAACCCTAAGTTCTACTGATCCTAAGGAGCGCTAAGGGGAATCGAAGGGCAAACTCCATCTTGGCAATTCCCATCGCCGCCGCCGTACTGTG[T/A]
TCTTCATCACCAGCACCCTACGACCGCAACACACGTTACCTTGGTGCCAACAACGACTAAAGCCGGCACTAATGTCCTCATCAAGCACCGATCAGTGCCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.90% 30.70% 0.23% 16.23% NA
All Indica  2759 81.70% 8.90% 0.14% 9.31% NA
All Japonica  1512 2.60% 77.50% 0.33% 19.58% NA
Aus  269 40.90% 1.10% 0.00% 57.99% NA
Indica I  595 81.20% 7.10% 0.17% 11.60% NA
Indica II  465 86.90% 9.70% 0.00% 3.44% NA
Indica III  913 84.70% 6.90% 0.00% 8.43% NA
Indica Intermediate  786 75.40% 12.10% 0.38% 12.09% NA
Temperate Japonica  767 0.30% 90.20% 0.00% 9.52% NA
Tropical Japonica  504 6.00% 54.80% 0.79% 38.49% NA
Japonica Intermediate  241 2.90% 84.60% 0.41% 12.03% NA
VI/Aromatic  96 52.10% 1.00% 0.00% 46.88% NA
Intermediate  90 51.10% 32.20% 2.22% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0405797011 A -> DEL N N silent_mutation Average:42.513; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0405797011 A -> T LOC_Os04g10660-LOC_Os04g10680 intergenic_region ; MODIFIER silent_mutation Average:42.513; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405797011 NA 1.01E-10 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0405797011 NA 2.08E-15 mr1035 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
vg0405797011 NA 7.72E-15 mr1062 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
vg0405797011 NA 1.97E-06 mr1090 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
vg0405797011 NA 5.80E-06 mr1134 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
vg0405797011 4.55E-06 NA mr1525 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
vg0405797011 NA 2.33E-13 mr1626 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
vg0405797011 NA 3.06E-26 mr1631 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
vg0405797011 4.53E-06 1.40E-07 mr1682 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
vg0405797011 NA 1.47E-15 mr1035_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
vg0405797011 2.20E-07 1.73E-07 mr1062_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
vg0405797011 4.27E-07 3.09E-06 mr1525_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