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Detailed information for vg0313930936:

Variant ID: vg0313930936 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 13930936
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


TTAATTGTGTACTGATGTATGGTCACAACTGTCACAAATAAATGGAGCGGAGGTGTTTTACAGCATTATCTGATTATCTCAACTATATAAATCAACATAT[A/G]
GTAGTGGTGGAGGCAGTATGCCATCCCACTACCACCACTTGAATATCAGTATCTTCTGTGGATAGATATAAGACTCTATTTGTATGGTGATGTTTTGGTG

Reverse complement sequence

CACCAAAACATCACCATACAAATAGAGTCTTATATCTATCCACAGAAGATACTGATATTCAAGTGGTGGTAGTGGGATGGCATACTGCCTCCACCACTAC[T/C]
ATATGTTGATTTATATAGTTGAGATAATCAGATAATGCTGTAAAACACCTCCGCTCCATTTATTTGTGACAGTTGTGACCATACATCAGTACACAATTAA

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 66.30% 33.70% 0.00% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 12.50% 87.50% 0.00% 0.00% NA
Aus  269 63.20% 36.80% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.10% 1.90% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 22.60% 77.40% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 5.00% 95.00% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 53.30% 46.70% 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
vg0313930936 A -> G LOC_Os03g24450.1 intron_variant ; MODIFIER silent_mutation Average:52.485; most accessible tissue: Callus, score: 69.197 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0313930936 NA 1.52E-06 mr1028 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
vg0313930936 NA 4.00E-10 mr1648 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
vg0313930936 NA 1.94E-08 mr1648 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
vg0313930936 1.40E-06 6.27E-11 mr1697 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
vg0313930936 NA 5.95E-06 mr1510_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
vg0313930936 NA 2.88E-21 mr1551_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
vg0313930936 NA 1.84E-12 mr1713_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