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Detailed information for vg0807835171:

Variant ID: vg0807835171 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7835171
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: 345. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGGTGAGAACCATCTTTGACATCAGGATGTTGGATCAATATACCGACGACTCGTCTTGCGTTCTGGTCTCGACTACGAACAACACACGGAGAGTGTTC[G/A]
GCACGACTAATTTCAAAAGCAAATGTCTCGTGTGGGGTAGTAAGAATTTCATCAGGAGGAGTGAGCTGGAGGGATCGGTTTATCTGCGCGACGACCGACT

Reverse complement sequence

AGTCGGTCGTCGCGCAGATAAACCGATCCCTCCAGCTCACTCCTCCTGATGAAATTCTTACTACCCCACACGAGACATTTGCTTTTGAAATTAGTCGTGC[C/T]
GAACACTCTCCGTGTGTTGTTCGTAGTCGAGACCAGAACGCAAGACGAGTCGTCGGTATATTGATCCAACATCCTGATGTCAAAGATGGTTCTCACCTCG

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 97.50% 2.10% 0.36% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.30% 6.50% 1.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 79.60% 17.50% 2.98% 0.00% NA
Japonica Intermediate  241 94.60% 4.60% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg0807835171 G -> A LOC_Os08g13180.1 missense_variant ; p.Gly126Ser; MODERATE nonsynonymous_codon ; G126S Average:63.41; most accessible tissue: Zhenshan97 panicle, score: 79.071 unknown unknown TOLERATED 0.84

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807835171 1.53E-06 1.30E-07 mr1218 Jap_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
vg0807835171 NA 5.36E-06 mr1794 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
vg0807835171 NA 6.14E-06 mr1068_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
vg0807835171 NA 1.73E-06 mr1096_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
vg0807835171 NA 3.33E-06 mr1121_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