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Detailed information for vg0402384313:

Variant ID: vg0402384313 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2384313
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.01, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TGACCTTCCTCGGTAGCATTCGCTCTCAGTGGTTTCGCTCGGAGGTCCCCACGGTCGGCACCAGCTGTTGTCGAAACGATAACCGCATACGTCGAAAGAC[A/G]
TGGTTACTCAACAGTGGTTGGAAAGAAATGAAGTGTATTAAGTTTTAGAGTTTTTTACTCCGGATCCCCCATTACATGGCCCTAGGGGACTATTTATAGC

Reverse complement sequence

GCTATAAATAGTCCCCTAGGGCCATGTAATGGGGGATCCGGAGTAAAAAACTCTAAAACTTAATACACTTCATTTCTTTCCAACCACTGTTGAGTAACCA[T/C]
GTCTTTCGACGTATGCGGTTATCGTTTCGACAACAGCTGGTGCCGACCGTGGGGACCTCCGAGCGAAACCACTGAGAGCGAATGCTACCGAGGAAGGTCA

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 16.40% 12.50% 24.74% 46.40% NA
All Indica  2759 7.10% 2.80% 27.55% 62.56% NA
All Japonica  1512 31.90% 33.10% 10.45% 24.60% NA
Aus  269 14.10% 1.10% 65.80% 18.96% NA
Indica I  595 4.70% 0.20% 21.51% 73.61% NA
Indica II  465 6.50% 4.10% 17.42% 72.04% NA
Indica III  913 8.70% 2.60% 33.73% 54.98% NA
Indica Intermediate  786 7.50% 4.20% 30.92% 57.38% NA
Temperate Japonica  767 29.10% 59.10% 8.60% 3.26% NA
Tropical Japonica  504 32.50% 2.60% 15.87% 49.01% NA
Japonica Intermediate  241 39.40% 14.10% 4.98% 41.49% NA
VI/Aromatic  96 36.50% 0.00% 43.75% 19.79% NA
Intermediate  90 25.60% 11.10% 35.56% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402384313 A -> DEL N N silent_mutation Average:19.627; most accessible tissue: Minghui63 young leaf, score: 26.082 N N N N
vg0402384313 A -> G LOC_Os04g04940.1 upstream_gene_variant ; 148.0bp to feature; MODIFIER silent_mutation Average:19.627; most accessible tissue: Minghui63 young leaf, score: 26.082 N N N N
vg0402384313 A -> G LOC_Os04g04940-LOC_Os04g04950 intergenic_region ; MODIFIER silent_mutation Average:19.627; most accessible tissue: Minghui63 young leaf, score: 26.082 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402384313 5.41E-07 NA mr1037 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
vg0402384313 2.37E-06 3.38E-13 mr1037 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
vg0402384313 1.99E-10 NA mr1798 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
vg0402384313 2.38E-11 4.45E-22 mr1798 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
vg0402384313 4.98E-08 NA mr1037_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
vg0402384313 2.01E-10 1.28E-13 mr1037_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
vg0402384313 NA 5.34E-07 mr1521_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
vg0402384313 NA 2.12E-06 mr1561_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
vg0402384313 2.19E-06 2.19E-06 mr1597_2 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
vg0402384313 NA 7.35E-06 mr1693_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
vg0402384313 3.96E-22 NA mr1798_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
vg0402384313 3.82E-24 1.08E-49 mr1798_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
vg0402384313 7.86E-07 2.34E-08 mr1798_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