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Detailed information for vg0701714318:

Variant ID: vg0701714318 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 1714318
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, C: 0.09, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


GTCAAGTGTCAACAACTAGAGTTTAATTAGCCGATACCAAGGAGAAGAGAAATCTTGATATGGATTAAATTAAGAAGAGATTTAGGTAATTTGAGCCAGA[G/C]
CAGACCCGAACAGAGGTTTTTAGTTCAGTGAACACACGGGAAGATCGGCCTCGATATATATATTTTGTGATTTTATTATTTTGCGGTTTCATTTAGACTT

Reverse complement sequence

AAGTCTAAATGAAACCGCAAAATAATAAAATCACAAAATATATATATCGAGGCCGATCTTCCCGTGTGTTCACTGAACTAAAAACCTCTGTTCGGGTCTG[C/G]
TCTGGCTCAAATTACCTAAATCTCTTCTTAATTTAATCCATATCAAGATTTCTCTTCTCCTTGGTATCGGCTAATTAAACTCTAGTTGTTGACACTTGAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.20% 32.70% 0.06% 0.00% NA
All Indica  2759 46.70% 53.30% 0.00% 0.00% NA
All Japonica  1512 97.80% 2.00% 0.20% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 39.30% 60.70% 0.00% 0.00% NA
Indica II  465 56.60% 43.40% 0.00% 0.00% NA
Indica III  913 45.10% 54.90% 0.00% 0.00% NA
Indica Intermediate  786 48.30% 51.70% 0.00% 0.00% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.60% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 1.20% 0.83% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg0701714318 G -> C LOC_Os07g04040.1 3_prime_UTR_variant ; 105.0bp to feature; MODIFIER silent_mutation Average:66.915; most accessible tissue: Callus, score: 87.539 N N N N
vg0701714318 G -> C LOC_Os07g04050.1 upstream_gene_variant ; 1542.0bp to feature; MODIFIER silent_mutation Average:66.915; most accessible tissue: Callus, score: 87.539 N N N N
vg0701714318 G -> C LOC_Os07g04060.1 downstream_gene_variant ; 3204.0bp to feature; MODIFIER silent_mutation Average:66.915; most accessible tissue: Callus, score: 87.539 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0701714318 NA 1.05E-08 mr1707 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
vg0701714318 2.19E-06 NA mr1721 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
vg0701714318 4.67E-06 NA mr1721 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
vg0701714318 NA 7.64E-08 mr1728 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
vg0701714318 NA 3.38E-12 mr1744 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
vg0701714318 NA 2.16E-08 mr1707_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