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Detailed information for vg0911777445:

Variant ID: vg0911777445 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 11777445
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, G: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


AAGATATATTTCCTCTATTTGTCCTATACCCCAATCGTCCATTTCGAATGAGTGAATAGCTGGTATCAATTCCTATAGCAAGTTGAACCCTCCACTTTTC[C/G]
TCCACAAATCTTTCAAACTCAGAAGAAGAACATTAGGACGAGCCCATCATGAGTATGCTACTGACCCCTTTGAAGCGCAAGAAATTTTCGTGACACGGAT

Reverse complement sequence

ATCCGTGTCACGAAAATTTCTTGCGCTTCAAAGGGGTCAGTAGCATACTCATGATGGGCTCGTCCTAATGTTCTTCTTCTGAGTTTGAAAGATTTGTGGA[G/C]
GAAAAGTGGAGGGTTCAACTTGCTATAGGAATTGATACCAGCTATTCACTCATTCGAAATGGACGATTGGGGTATAGGACAAATAGAGGAAATATATCTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.40% 11.60% 0.02% 0.00% NA
All Indica  2759 80.50% 19.50% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 81.70% 18.30% 0.00% 0.00% NA
Indica II  465 82.60% 17.40% 0.00% 0.00% NA
Indica III  913 81.50% 18.50% 0.00% 0.00% NA
Indica Intermediate  786 77.10% 22.80% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0911777445 C -> G LOC_Os09g19670-LOC_Os09g19690 intergenic_region ; MODIFIER silent_mutation Average:67.575; most accessible tissue: Callus, score: 87.658 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0911777445 NA 3.44E-06 mr1125 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
vg0911777445 NA 2.32E-06 mr1522 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
vg0911777445 NA 8.28E-07 mr1522_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
vg0911777445 NA 5.85E-08 mr1522_2 Ind_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