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

Detailed information for vg0516238439:

Variant ID: vg0516238439 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 16238439
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.71, C: 0.30, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


CCCGTTACGATGTGTATCTACAACCTCCCCCCTGGCTATGCATGAAGAGGAAGTACATAATGATGCCGATTATTATTCAAGGCCCCAAGCAACTTGGTAA[C/T]
GACTTCGATGTGTACCTAAGACCACTGGTCGAAGATCTTAAACTGTTGTGGAAGAAGGAAGGTGTCCCCGTGTGGGACGAGGACAAACAGGAGGAGTTTA

Reverse complement sequence

TAAACTCCTCCTGTTTGTCCTCGTCCCACACGGGGACACCTTCCTTCTTCCACAACAGTTTAAGATCTTCGACCAGTGGTCTTAGGTACACATCGAAGTC[G/A]
TTACCAAGTTGCTTGGGGCCTTGAATAATAATCGGCATCATTATGTACTTCCTCTTCATGCATAGCCAGGGGGGAGGTTGTAGATACACATCGTAACGGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.90% 25.90% 1.21% 0.00% NA
All Indica  2759 96.60% 1.40% 2.03% 0.00% NA
All Japonica  1512 24.70% 75.30% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 96.60% 1.20% 2.18% 0.00% NA
Indica II  465 96.80% 1.70% 1.51% 0.00% NA
Indica III  913 97.40% 1.00% 1.64% 0.00% NA
Indica Intermediate  786 95.40% 1.90% 2.67% 0.00% NA
Temperate Japonica  767 7.00% 93.00% 0.00% 0.00% NA
Tropical Japonica  504 53.40% 46.60% 0.00% 0.00% NA
Japonica Intermediate  241 20.70% 78.80% 0.41% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg0516238439 C -> T LOC_Os05g27850.1 synonymous_variant ; p.Asn264Asn; LOW synonymous_codon Average:15.652; most accessible tissue: Zhenshan97 flag leaf, score: 21.009 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0516238439 NA 5.87E-14 Grain_width Jap_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
vg0516238439 4.85E-06 4.85E-06 mr1153 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
vg0516238439 2.29E-06 NA mr1176 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
vg0516238439 1.02E-06 1.57E-06 mr1176 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
vg0516238439 NA 1.01E-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
vg0516238439 7.55E-06 7.55E-06 mr1355 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
vg0516238439 8.06E-06 8.06E-06 mr1357 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
vg0516238439 6.01E-06 4.95E-06 mr1406 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
vg0516238439 3.54E-06 3.54E-06 mr1506 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
vg0516238439 NA 4.44E-17 mr1699 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
vg0516238439 6.03E-06 NA mr1732 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
vg0516238439 NA 2.57E-14 mr1771 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
vg0516238439 NA 6.88E-37 mr1784 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
vg0516238439 NA 1.18E-10 mr1790 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
vg0516238439 NA 1.15E-07 mr1800 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
vg0516238439 NA 1.84E-06 mr1248_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
vg0516238439 NA 8.44E-10 mr1771_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