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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0523035315:

Variant ID: vg0523035315 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 23035315
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


AGCCGATTGACTTCTCACCAGCCGATAAATATAACCTAAACGGTATCCCTTTCTGTGGAGGAATCAAAACAGGAGGAGAGCTGAGATACTCCTTGATATT[A/T]
TCCAAAGCCTTTTGCTGCTCTGCCCCCCAAGTGAATTGCTGATTGGCTTTTAATTTCAATAAGGGTGTAAAAGGTTCCAACCTCCTGGACAAATTTGAAA

Reverse complement sequence

TTTCAAATTTGTCCAGGAGGTTGGAACCTTTTACACCCTTATTGAAATTAAAAGCCAATCAGCAATTCACTTGGGGGGCAGAGCAGCAAAAGGCTTTGGA[T/A]
AATATCAAGGAGTATCTCAGCTCTCCTCCTGTTTTGATTCCTCCACAGAAAGGGATACCGTTTAGGTTATATTTATCGGCTGGTGAGAAGTCAATCGGCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 1.60% 1.33% 0.00% NA
All Indica  2759 99.80% 0.10% 0.11% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 65.40% 16.70% 17.84% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 99.60% 0.30% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 65.60% 25.00% 9.38% 0.00% NA
Intermediate  90 94.40% 2.20% 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
vg0523035315 A -> T LOC_Os05g39280.1 missense_variant ; p.Asp775Glu; MODERATE nonsynonymous_codon ; D775E Average:35.799; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 benign 0.784 TOLERATED 0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0523035315 8.86E-06 6.52E-06 mr1685 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
vg0523035315 NA 7.43E-10 mr1057_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
vg0523035315 NA 4.26E-08 mr1126_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
vg0523035315 NA 7.25E-06 mr1127_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
vg0523035315 NA 3.92E-11 mr1166_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
vg0523035315 NA 1.75E-08 mr1465_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
vg0523035315 NA 2.94E-07 mr1585_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
vg0523035315 NA 2.72E-06 mr1603_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
vg0523035315 9.74E-07 5.72E-16 mr1612_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
vg0523035315 NA 1.14E-06 mr1662_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
vg0523035315 4.16E-06 NA mr1915_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
vg0523035315 2.38E-06 NA mr1940_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