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Detailed information for vg0907602051:

Variant ID: vg0907602051 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7602051
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


CCACCGCAAACCCTAGCCGCTGACGCAATAATTCCCTTTTTCCTTTTCAAAAATAATTCATTATTGCGTCATAATTCAATTAAAATCCATATAAGTGTTT[C/T]
AATCCGATTAAATCTTCAAAAATTCATAACTAATTCATCTTAGCTCGGATTTAGTTGGTTCAAGTCTCTAAATTTTTCTAAAATTGAGGTCTACATGTTA

Reverse complement sequence

TAACATGTAGACCTCAATTTTAGAAAAATTTAGAGACTTGAACCAACTAAATCCGAGCTAAGATGAATTAGTTATGAATTTTTGAAGATTTAATCGGATT[G/A]
AAACACTTATATGGATTTTAATTGAATTATGACGCAATAATGAATTATTTTTGAAAAGGAAAAAGGGAATTATTGCGTCAGCGGCTAGGGTTTGCGGTGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 11.90% 11.96% 20.12% NA
All Indica  2759 35.20% 20.20% 17.58% 27.00% NA
All Japonica  1512 92.50% 0.10% 0.66% 6.75% NA
Aus  269 40.50% 1.10% 24.91% 33.46% NA
Indica I  595 56.50% 12.10% 9.58% 21.85% NA
Indica II  465 38.90% 6.90% 10.75% 43.44% NA
Indica III  913 13.30% 39.10% 28.37% 19.28% NA
Indica Intermediate  786 42.50% 12.20% 15.14% 30.15% NA
Temperate Japonica  767 87.90% 0.10% 1.04% 10.95% NA
Tropical Japonica  504 97.40% 0.20% 0.20% 2.18% NA
Japonica Intermediate  241 96.70% 0.00% 0.41% 2.90% NA
VI/Aromatic  96 96.90% 1.00% 1.04% 1.04% NA
Intermediate  90 82.20% 1.10% 2.22% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0907602051 C -> DEL N N silent_mutation Average:34.517; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0907602051 C -> T LOC_Os09g13190.1 upstream_gene_variant ; 2755.0bp to feature; MODIFIER silent_mutation Average:34.517; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0907602051 C -> T LOC_Os09g13190-LOC_Os09g13200 intergenic_region ; MODIFIER silent_mutation Average:34.517; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907602051 1.95E-06 NA mr1008 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
vg0907602051 3.85E-06 NA mr1009 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
vg0907602051 NA 2.82E-09 mr1198 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
vg0907602051 NA 2.02E-07 mr1604 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
vg0907602051 NA 4.09E-06 mr1020_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
vg0907602051 NA 7.02E-16 mr1416_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