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Detailed information for vg0100791519:

Variant ID: vg0100791519 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 791519
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


AATGAAGAGATACATTTGAAGGTCGAAATGTTTCTCAAGACATATGGCACATCGAAACCCACAAGGTATAGTTTCTCTGAAGTTAAGAAGATTACAAGAC[G/A]
GTTCAGGGAAAAGATAGGCCACGGTGGGTATGGAAATGTATACAAGGGTGAGCTACCAAATGGAGTGCCCGTGGCAGTTAAGATGCTAGAAAATTCCAGA

Reverse complement sequence

TCTGGAATTTTCTAGCATCTTAACTGCCACGGGCACTCCATTTGGTAGCTCACCCTTGTATACATTTCCATACCCACCGTGGCCTATCTTTTCCCTGAAC[C/T]
GTCTTGTAATCTTCTTAACTTCAGAGAAACTATACCTTGTGGGTTTCGATGTGCCATATGTCTTGAGAAACATTTCGACCTTCAAATGTATCTCTTCATT

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 49.40% 22.70% 1.02% 26.94% NA
All Indica  2759 38.30% 21.60% 1.30% 38.78% NA
All Japonica  1512 68.80% 28.50% 0.13% 2.58% NA
Aus  269 47.60% 4.10% 2.23% 46.10% NA
Indica I  595 3.70% 66.70% 0.34% 29.24% NA
Indica II  465 73.10% 4.10% 1.08% 21.72% NA
Indica III  913 38.30% 3.30% 1.42% 56.96% NA
Indica Intermediate  786 43.90% 19.10% 2.04% 34.99% NA
Temperate Japonica  767 93.40% 2.00% 0.00% 4.69% NA
Tropical Japonica  504 22.20% 77.00% 0.40% 0.40% NA
Japonica Intermediate  241 88.00% 11.60% 0.00% 0.41% NA
VI/Aromatic  96 60.40% 7.30% 2.08% 30.21% NA
Intermediate  90 55.60% 30.00% 2.22% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0100791519 G -> A LOC_Os01g02440.1 missense_variant ; p.Arg265Gln; MODERATE nonsynonymous_codon ; R265Q Average:53.74; most accessible tissue: Zhenshan97 panicle, score: 68.538 probably damaging 2.117 TOLERATED 0.50
vg0100791519 G -> DEL LOC_Os01g02440.1 N frameshift_variant Average:53.74; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0100791519 NA 5.29E-09 mr1059 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
vg0100791519 NA 3.00E-11 mr1143 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
vg0100791519 NA 7.20E-10 mr1167 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
vg0100791519 NA 9.56E-10 mr1535 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
vg0100791519 NA 5.73E-09 mr1593 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
vg0100791519 NA 8.38E-10 mr1675 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
vg0100791519 NA 2.11E-07 mr1726 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
vg0100791519 NA 5.87E-08 mr1739 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
vg0100791519 NA 3.48E-08 mr1739 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
vg0100791519 NA 6.29E-07 mr1950 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
vg0100791519 NA 6.70E-10 mr1969 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
vg0100791519 NA 1.39E-11 mr1995 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
vg0100791519 NA 3.39E-06 mr1158_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
vg0100791519 NA 8.58E-09 mr1167_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
vg0100791519 NA 8.52E-06 mr1360_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
vg0100791519 NA 1.57E-06 mr1378_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
vg0100791519 NA 5.23E-08 mr1383_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
vg0100791519 NA 2.72E-07 mr1458_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
vg0100791519 NA 1.68E-10 mr1593_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
vg0100791519 NA 3.00E-06 mr1726_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
vg0100791519 NA 5.11E-10 mr1739_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
vg0100791519 NA 5.91E-11 mr1794_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