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Detailed information for vg0320914714:

Variant ID: vg0320914714 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20914714
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:


GGCAGGGAAATACGGTGTTTCTTGATTTTGAGCTGCCTGTCGACCATTCAGTACAGTTCAACACATCTTCGAAAACAAGGCGTTTGAGCTTTGGGAACAT[G/A]
ATCTGATCTGATCGTTGAGGAACAGTGTTCACCTTGTTGACAGAATGGATTTTTCTCATCTCGAGAATCTCAAGGCAGGGCATGATATGGAATGGAGGGA

Reverse complement sequence

TCCCTCCATTCCATATCATGCCCTGCCTTGAGATTCTCGAGATGAGAAAAATCCATTCTGTCAACAAGGTGAACACTGTTCCTCAACGATCAGATCAGAT[C/T]
ATGTTCCCAAAGCTCAAACGCCTTGTTTTCGAAGATGTGTTGAACTGTACTGAATGGTCGACAGGCAGCTCAAAATCAAGAAACACCGTATTTCCCTGCC

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 94.50% 5.30% 0.21% 0.00% NA
All Indica  2759 99.20% 0.70% 0.11% 0.00% NA
All Japonica  1512 91.60% 8.10% 0.26% 0.00% NA
Aus  269 88.80% 10.80% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 1.70% 0.38% 0.00% NA
Temperate Japonica  767 98.70% 1.20% 0.13% 0.00% NA
Tropical Japonica  504 79.40% 20.20% 0.40% 0.00% NA
Japonica Intermediate  241 94.60% 5.00% 0.41% 0.00% NA
VI/Aromatic  96 28.10% 69.80% 2.08% 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
vg0320914714 G -> A LOC_Os03g37720.1 synonymous_variant ; p.Ile899Ile; LOW synonymous_codon Average:60.619; most accessible tissue: Zhenshan97 young leaf, score: 79.507 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320914714 NA 1.36E-08 mr1217 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
vg0320914714 NA 1.16E-07 mr1845 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
vg0320914714 NA 6.16E-06 mr1126_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
vg0320914714 4.74E-07 NA mr1750_2 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
vg0320914714 2.71E-06 NA mr1987_2 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