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Detailed information for vg0406853685:

Variant ID: vg0406853685 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6853685
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAAAGAAGAAGAAGAGAACCGCAAGAGCAAGAGCAAGGCAGAGATCGATGATGAAGAGATGGCTCTCTTCGTCAAGAAGTTCAGCAAGTTCATGAGGC[G/A]
AAGCGGCTTCTTCAAGGGAGGTTCTTCCAACCACTACTCCAACAAGTCAAGTGGAAGACACTCCACAAGAGTGTGCTACGTGTGCAAAGAGCCCGGGCAC

Reverse complement sequence

GTGCCCGGGCTCTTTGCACACGTAGCACACTCTTGTGGAGTGTCTTCCACTTGACTTGTTGGAGTAGTGGTTGGAAGAACCTCCCTTGAAGAAGCCGCTT[C/T]
GCCTCATGAACTTGCTGAACTTCTTGACGAAGAGAGCCATCTCTTCATCATCGATCTCTGCCTTGCTCTTGCTCTTGCGGTTCTCTTCTTCTTCTTTCTT

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 74.20% 11.00% 3.77% 11.02% NA
All Indica  2759 62.50% 18.30% 5.80% 13.45% NA
All Japonica  1512 95.80% 0.30% 0.46% 3.44% NA
Aus  269 71.70% 0.00% 2.97% 25.28% NA
Indica I  595 77.10% 6.10% 3.19% 13.61% NA
Indica II  465 71.00% 15.50% 1.29% 12.26% NA
Indica III  913 49.90% 23.70% 11.39% 15.01% NA
Indica Intermediate  786 60.80% 23.00% 3.94% 12.21% NA
Temperate Japonica  767 97.10% 0.10% 0.00% 2.74% NA
Tropical Japonica  504 95.40% 0.80% 0.99% 2.78% NA
Japonica Intermediate  241 92.10% 0.00% 0.83% 7.05% NA
VI/Aromatic  96 74.00% 0.00% 3.12% 22.92% NA
Intermediate  90 81.10% 10.00% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0406853685 G -> DEL LOC_Os04g12410.1 N frameshift_variant Average:27.265; most accessible tissue: Minghui63 flag leaf, score: 47.544 N N N N
vg0406853685 G -> A LOC_Os04g12410.1 missense_variant ; p.Arg286Gln; MODERATE nonsynonymous_codon ; R286Q Average:27.265; most accessible tissue: Minghui63 flag leaf, score: 47.544 benign 0.107 TOLERATED 0.27

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406853685 NA 2.81E-06 mr1015 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
vg0406853685 5.12E-06 4.82E-06 mr1054 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
vg0406853685 4.99E-06 4.99E-06 mr1054 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
vg0406853685 NA 8.01E-06 mr1287 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
vg0406853685 8.82E-06 8.82E-06 mr1287 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
vg0406853685 NA 5.79E-06 mr1305 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
vg0406853685 NA 6.16E-06 mr1314 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
vg0406853685 NA 6.48E-06 mr1320 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
vg0406853685 NA 6.63E-06 mr1372 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
vg0406853685 NA 4.96E-06 mr1372 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
vg0406853685 NA 3.19E-06 mr1409 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
vg0406853685 NA 1.88E-06 mr1515 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
vg0406853685 NA 2.06E-06 mr1537 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
vg0406853685 3.03E-06 NA mr1661 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
vg0406853685 7.61E-06 4.13E-06 mr1687 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
vg0406853685 5.96E-06 1.80E-06 mr1972 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
vg0406853685 9.04E-06 9.04E-06 mr1972 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