Search for Variation information by Variation ID:

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

Detailed information for vg0714252091:

Variant ID: vg0714252091 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 14252091
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


ACATCCCACCAATGATGTAAACACATGCAGGACCCACACACACAACCAAACTTAAGCAAGCAAACTAACACAACGATCTAAGGCAATGACTTAGCACAAC[G/A]
GTCTAGGTCTTCCGGGCATCGGAGTTGATTGAAGGCTCGTTCGGCACGTCCCCATCATCTTGAGTTGGTCCCCACTCGATCTTGGAATGGGTGCGCTTGG

Reverse complement sequence

CCAAGCGCACCCATTCCAAGATCGAGTGGGGACCAACTCAAGATGATGGGGACGTGCCGAACGAGCCTTCAATCAACTCCGATGCCCGGAAGACCTAGAC[C/T]
GTTGTGCTAAGTCATTGCCTTAGATCGTTGTGTTAGTTTGCTTGCTTAAGTTTGGTTGTGTGTGTGGGTCCTGCATGTGTTTACATCATTGGTGGGATGT

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 65.30% 23.70% 8.08% 2.98% NA
All Indica  2759 53.30% 34.80% 10.62% 1.30% NA
All Japonica  1512 78.90% 9.30% 4.89% 6.88% NA
Aus  269 98.10% 0.70% 1.12% 0.00% NA
Indica I  595 71.40% 18.20% 9.58% 0.84% NA
Indica II  465 38.70% 48.80% 11.83% 0.65% NA
Indica III  913 49.10% 39.80% 8.87% 2.30% NA
Indica Intermediate  786 53.10% 33.30% 12.72% 0.89% NA
Temperate Japonica  767 86.60% 0.90% 1.56% 10.95% NA
Tropical Japonica  504 70.20% 20.40% 7.34% 1.98% NA
Japonica Intermediate  241 72.60% 12.90% 10.37% 4.15% NA
VI/Aromatic  96 95.80% 2.10% 2.08% 0.00% NA
Intermediate  90 72.20% 15.60% 11.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0714252091 G -> DEL N N silent_mutation Average:17.297; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N
vg0714252091 G -> A LOC_Os07g25010.1 intron_variant ; MODIFIER silent_mutation Average:17.297; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0714252091 NA 5.99E-06 mr1035 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
vg0714252091 1.75E-06 4.49E-09 mr1053 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
vg0714252091 2.10E-07 8.70E-07 mr1053 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
vg0714252091 1.26E-06 1.33E-06 mr1147 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
vg0714252091 NA 1.24E-06 mr1279 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
vg0714252091 NA 4.45E-11 mr1709 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
vg0714252091 NA 7.97E-09 mr1709 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
vg0714252091 NA 2.30E-08 mr1709_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