Search for Variation information by Variation ID:

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

Detailed information for vg0725373324:

Variant ID: vg0725373324 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25373324
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, G: 0.31, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CAAAGAAGCCAAGGCTGGATACAAGAATTGGTTGTCCAGCGCGGTTGATTATTAAAGTCACACCAGAGAGTAAATACAGAGTCACTGACTTCAAAGCGGA[C/G]
CACAATCATCAGCTGGCCCCTCCTTCGACAATGCATATGTTAAGGTCACAGAGGATATTGACAGAACTTCAGTCTGGGGAAGCAGAATTGTCAGATGATT

Reverse complement sequence

AATCATCTGACAATTCTGCTTCCCCAGACTGAAGTTCTGTCAATATCCTCTGTGACCTTAACATATGCATTGTCGAAGGAGGGGCCAGCTGATGATTGTG[G/C]
TCCGCTTTGAAGTCAGTGACTCTGTATTTACTCTCTGGTGTGACTTTAATAATCAACCGCGCTGGACAACCAATTCTTGTATCCAGCCTTGGCTTCTTTG

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 61.80% 38.10% 0.04% 0.00% NA
All Indica  2759 94.90% 5.00% 0.04% 0.00% NA
All Japonica  1512 0.10% 99.90% 0.00% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 92.30% 7.70% 0.00% 0.00% NA
Indica II  465 92.90% 7.10% 0.00% 0.00% NA
Indica III  913 98.60% 1.40% 0.00% 0.00% NA
Indica Intermediate  786 93.90% 6.00% 0.13% 0.00% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 38.90% 60.00% 1.11% 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
vg0725373324 C -> G LOC_Os07g42400.1 missense_variant ; p.Asp215Glu; MODERATE nonsynonymous_codon ; D215E Average:47.181; most accessible tissue: Callus, score: 84.092 benign 0.07 TOLERATED 0.39
vg0725373324 C -> G LOC_Os07g42400.2 missense_variant ; p.Asp215Glu; MODERATE nonsynonymous_codon ; D215E Average:47.181; most accessible tissue: Callus, score: 84.092 benign 0.07 TOLERATED 0.31

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725373324 NA 2.45E-25 mr1039 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
vg0725373324 NA 1.03E-11 mr1070 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
vg0725373324 NA 4.17E-10 mr1128 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
vg0725373324 NA 1.12E-13 mr1386 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
vg0725373324 NA 2.10E-28 mr1414 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
vg0725373324 NA 1.00E-08 mr1514 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
vg0725373324 NA 5.19E-36 mr1542 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
vg0725373324 NA 1.70E-27 mr1632 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
vg0725373324 NA 9.04E-11 mr1683 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
vg0725373324 NA 1.30E-11 mr1751 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
vg0725373324 NA 3.91E-28 mr1039_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
vg0725373324 NA 2.03E-12 mr1128_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
vg0725373324 NA 3.51E-34 mr1632_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