Search for Variation information by Variation ID:

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

Detailed information for vg0625536742:

Variant ID: vg0625536742 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25536742
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


AGGATGATGGCGCCCCACCGCGAGCATGAATAGCTGCTTCCCATACACCTGGTACCCCCAGGATCTTCACCACCGTGCCAGGAAGGAGCTTCTCGATGTT[G/C]
TCACCCTCGAGGATGAGGAAGCTGATGGCGACAAGGTAGAGCTCGACTTATAAGACGAGGCCGATGGCCATCTAGCCGTAGCCGGCGAAGGCTAGGTACG

Reverse complement sequence

CGTACCTAGCCTTCGCCGGCTACGGCTAGATGGCCATCGGCCTCGTCTTATAAGTCGAGCTCTACCTTGTCGCCATCAGCTTCCTCATCCTCGAGGGTGA[C/G]
AACATCGAGAAGCTCCTTCCTGGCACGGTGGTGAAGATCCTGGGGGTACCAGGTGTATGGGAAGCAGCTATTCATGCTCGCGGTGGGGCGCCATCATCCT

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 91.00% 5.60% 3.39% 0.00% NA
All Indica  2759 97.60% 0.30% 2.10% 0.00% NA
All Japonica  1512 77.20% 16.20% 6.55% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.10% 0.00% 3.87% 0.00% NA
Indica II  465 97.80% 0.40% 1.72% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 0.80% 3.44% 0.00% NA
Temperate Japonica  767 89.60% 2.00% 8.47% 0.00% NA
Tropical Japonica  504 63.90% 32.90% 3.17% 0.00% NA
Japonica Intermediate  241 66.00% 26.60% 7.47% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 10.00% 3.33% 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
vg0625536742 G -> C LOC_Os06g42480.1 missense_variant ; p.Val26Leu; MODERATE nonsynonymous_codon ; V26L Average:69.979; most accessible tissue: Zhenshan97 young leaf, score: 83.199 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0625536742 NA 2.44E-06 mr1114 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
vg0625536742 NA 2.94E-06 mr1117 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
vg0625536742 NA 5.96E-06 mr1119 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
vg0625536742 6.85E-07 NA mr1240 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
vg0625536742 1.51E-06 8.77E-08 mr1240 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
vg0625536742 NA 8.44E-07 mr1496 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
vg0625536742 NA 3.68E-07 mr1602 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
vg0625536742 7.01E-07 NA mr1693 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