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Detailed information for vg0905340944:

Variant ID: vg0905340944 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5340944
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


GACGTCCACGCATCTGCGCGGGCTTCCATTCTAGTTCAATTAATGGCCAAAACTGGTACTGATACACGCAGAAAAATCGTCCCACCAACAAAACAGAATG[A/G]
CCCATTGTTTCGTTTTTGTCCGTTACAGTCAACACAGCTGCACTCATAAAATCAAGTAACGCAACTGTCAAACGCAGGGCATAGTCATAGTGCCGGGTTT

Reverse complement sequence

AAACCCGGCACTATGACTATGCCCTGCGTTTGACAGTTGCGTTACTTGATTTTATGAGTGCAGCTGTGTTGACTGTAACGGACAAAAACGAAACAATGGG[T/C]
CATTCTGTTTTGTTGGTGGGACGATTTTTCTGCGTGTATCAGTACCAGTTTTGGCCATTAATTGAACTAGAATGGAAGCCCGCGCAGATGCGTGGACGTC

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 71.40% 28.60% 0.00% 0.00% NA
All Indica  2759 98.10% 1.90% 0.00% 0.00% NA
All Japonica  1512 20.30% 79.70% 0.00% 0.00% NA
Aus  269 78.10% 21.90% 0.00% 0.00% NA
Indica I  595 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 10.70% 89.30% 0.00% 0.00% NA
Tropical Japonica  504 18.50% 81.50% 0.00% 0.00% NA
Japonica Intermediate  241 54.80% 45.20% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 62.20% 37.80% 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
vg0905340944 A -> G LOC_Os09g09830-LOC_Os09g09850 intergenic_region ; MODIFIER silent_mutation Average:70.259; most accessible tissue: Callus, score: 92.436 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905340944 NA 6.01E-13 mr1010 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
vg0905340944 2.06E-06 1.38E-15 mr1034 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
vg0905340944 NA 7.55E-22 mr1163 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
vg0905340944 NA 2.76E-08 mr1700_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