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Detailed information for vg0809871494:

Variant ID: vg0809871494 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 9871494
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


CCAAGCGCCACAAACAGTGGCGGAAGGGGCTTCGGCTCTTCAGGCGCAACTCCAAACTTTCCTTCAGCAACTCAACCAACCCCACTGCATTTCAAGTACA[A/G]
CCCCATCGGCCCACCCGGAGGGGAATACAAGTCAAGGTGCGCCTAATTGGTTGCCACCGATTCAGCCGGGCCTGGGAGTTTCGCCGTGGAATCAAGGACC

Reverse complement sequence

GGTCCTTGATTCCACGGCGAAACTCCCAGGCCCGGCTGAATCGGTGGCAACCAATTAGGCGCACCTTGACTTGTATTCCCCTCCGGGTGGGCCGATGGGG[T/C]
TGTACTTGAAATGCAGTGGGGTTGGTTGAGTTGCTGAAGGAAAGTTTGGAGTTGCGCCTGAAGAGCCGAAGCCCCTTCCGCCACTGTTTGTGGCGCTTGG

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 90.90% 9.10% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 72.80% 27.20% 0.00% 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 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 97.80% 2.20% 0.00% 0.00% NA
Tropical Japonica  504 44.20% 55.80% 0.00% 0.00% NA
Japonica Intermediate  241 52.70% 47.30% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0809871494 A -> G LOC_Os08g16190.1 missense_variant ; p.Thr234Ala; MODERATE nonsynonymous_codon ; T234A Average:57.446; most accessible tissue: Zhenshan97 flag leaf, score: 84.295 benign 0.781 TOLERATED 0.32

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0809871494 NA 3.60E-07 mr1040 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
vg0809871494 NA 1.26E-08 mr1045 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
vg0809871494 NA 9.04E-06 mr1095 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
vg0809871494 NA 2.55E-09 mr1194 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
vg0809871494 NA 4.52E-06 mr1482 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
vg0809871494 NA 3.11E-06 mr1521 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
vg0809871494 NA 1.06E-07 mr1668 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
vg0809871494 NA 1.74E-07 mr1746 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
vg0809871494 NA 5.51E-07 mr1194_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