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Detailed information for vg0907965825:

Variant ID: vg0907965825 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7965825
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TATATGCAACTAATCCTTTAATTAATTAAAAACGAAGAGTACAGGCGGATTTCCTTTGATGCTCACACGTGAGATATATACATATAACTACAAAAAGAAT[A/G]
TCTAAACGATTCTTAATTTCCTCTCTGAACGATGCTTGAAATTTTGTCTCAAAACATTAAAAAAATAATTTACCTAAAAAATGGTAAAATTTTGTAGTTC

Reverse complement sequence

GAACTACAAAATTTTACCATTTTTTAGGTAAATTATTTTTTTAATGTTTTGAGACAAAATTTCAAGCATCGTTCAGAGAGGAAATTAAGAATCGTTTAGA[T/C]
ATTCTTTTTGTAGTTATATGTATATATCTCACGTGTGAGCATCAAAGGAAATCCGCCTGTACTCTTCGTTTTTAATTAATTAAAGGATTAGTTGCATATA

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 79.80% 20.10% 0.17% 0.00% NA
All Indica  2759 94.20% 5.70% 0.11% 0.00% NA
All Japonica  1512 48.40% 51.30% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.60% 4.20% 0.17% 0.00% NA
Indica II  465 88.80% 10.80% 0.43% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 90.70% 9.30% 0.00% 0.00% NA
Temperate Japonica  767 36.40% 63.20% 0.39% 0.00% NA
Tropical Japonica  504 76.80% 23.00% 0.20% 0.00% NA
Japonica Intermediate  241 27.40% 72.60% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 1.11% 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
vg0907965825 A -> G LOC_Os09g13650.1 intron_variant ; MODIFIER silent_mutation Average:30.97; most accessible tissue: Callus, score: 58.369 N N N N
vg0907965825 A -> G LOC_Os09g13650.2 intron_variant ; MODIFIER silent_mutation Average:30.97; most accessible tissue: Callus, score: 58.369 N N N N
vg0907965825 A -> G LOC_Os09g13650.3 intron_variant ; MODIFIER silent_mutation Average:30.97; most accessible tissue: Callus, score: 58.369 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907965825 2.26E-06 6.62E-13 mr1002 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
vg0907965825 6.62E-06 1.05E-13 mr1002 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
vg0907965825 NA 9.20E-10 mr1282 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
vg0907965825 NA 3.28E-09 mr1658 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
vg0907965825 NA 3.22E-14 mr1002_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
vg0907965825 NA 7.45E-11 mr1002_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
vg0907965825 NA 2.87E-07 mr1030_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
vg0907965825 NA 6.08E-06 mr1330_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
vg0907965825 NA 2.34E-06 mr1379_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
vg0907965825 NA 1.21E-06 mr1555_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
vg0907965825 NA 2.55E-08 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
vg0907965825 NA 4.09E-07 mr1748_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
vg0907965825 NA 4.11E-10 mr1805_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