\

Search for Variation information by Variation ID:

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

Detailed information for vg0719799826:

Variant ID: vg0719799826 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19799826
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGCCTCGCTCATCTAAGTTATCACCTAAGGTGGATGAGGGATTCTTACTTGGCTATGAATCAAATGCACATGCCTACCGTGTCTTCAACAAAACCTCT[A/G]
GTATTGTTGAAGTTACAAGGGATGTGACATTTGACGAATCTAATGGCTCCCAAGGAGAGCAAGTTGTTGTACATGTTGTAGATGATGCGGATCCTAGACA

Reverse complement sequence

TGTCTAGGATCCGCATCATCTACAACATGTACAACAACTTGCTCTCCTTGGGAGCCATTAGATTCGTCAAATGTCACATCCCTTGTAACTTCAACAATAC[T/C]
AGAGGTTTTGTTGAAGACACGGTAGGCATGTGCATTTGATTCATAGCCAAGTAAGAATCCCTCATCCACCTTAGGTGATAACTTAGATGAGCGAGGCCTC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.90% 28.20% 2.09% 3.83% NA
All Indica  2759 86.90% 8.70% 3.33% 1.12% NA
All Japonica  1512 41.70% 48.50% 0.33% 9.52% NA
Aus  269 11.20% 87.70% 0.00% 1.12% NA
Indica I  595 90.80% 0.30% 6.55% 2.35% NA
Indica II  465 90.30% 4.50% 4.09% 1.08% NA
Indica III  913 82.30% 15.80% 1.64% 0.33% NA
Indica Intermediate  786 87.30% 9.20% 2.42% 1.15% NA
Temperate Japonica  767 54.50% 45.40% 0.13% 0.00% NA
Tropical Japonica  504 12.70% 58.50% 0.79% 27.98% NA
Japonica Intermediate  241 61.40% 37.30% 0.00% 1.24% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 61.10% 33.30% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0719799826 A -> DEL LOC_Os07g33160.1 N frameshift_variant Average:6.608; most accessible tissue: Callus, score: 18.471 N N N N
vg0719799826 A -> G LOC_Os07g33160.1 missense_variant ; p.Ser144Gly; MODERATE nonsynonymous_codon ; S144G Average:6.608; most accessible tissue: Callus, score: 18.471 benign -0.699 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719799826 NA 6.57E-06 mr1029 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
vg0719799826 7.07E-06 NA mr1076_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
vg0719799826 1.80E-06 NA mr1083_2 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
vg0719799826 6.69E-06 NA mr1085_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
vg0719799826 5.66E-06 NA mr1301_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
vg0719799826 NA 9.26E-06 mr1402_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
vg0719799826 NA 2.89E-12 mr1409_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
vg0719799826 NA 3.95E-07 mr1548_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
vg0719799826 NA 1.70E-10 mr1649_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
vg0719799826 NA 4.88E-09 mr1709_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
vg0719799826 NA 2.72E-06 mr1762_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
vg0719799826 2.48E-06 9.73E-06 mr1888_2 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