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Detailed information for vg0123522936:

Variant ID: vg0123522936 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23522936
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTTTTATTGGACCGGAGCAAATTTCAACAAACAAACACTCCTATTGGCTCACTGACTGTAATATTGTTTGAAACGACTCACTGACTGTACCTAACCAC[A/G]
ATGATTCTTTTAGATAATGGAAATGGTTTATATCCCAGCACATAACCATGATGATTAATGATTAACAATCTCTGCAATCTGTTAAATTCTCCCTGGGAAA

Reverse complement sequence

TTTCCCAGGGAGAATTTAACAGATTGCAGAGATTGTTAATCATTAATCATCATGGTTATGTGCTGGGATATAAACCATTTCCATTATCTAAAAGAATCAT[T/C]
GTGGTTAGGTACAGTCAGTGAGTCGTTTCAAACAATATTACAGTCAGTGAGCCAATAGGAGTGTTTGTTTGTTGAAATTTGCTCCGGTCCAATAAAAAGT

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 90.50% 9.50% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 71.60% 28.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 55.10% 44.90% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.80% 0.00% 0.00% NA
Japonica Intermediate  241 70.50% 29.50% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0123522936 A -> G LOC_Os01g41560.1 synonymous_variant ; p.Ile207Ile; LOW synonymous_codon Average:45.618; most accessible tissue: Zhenshan97 flower, score: 60.301 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123522936 NA 8.85E-10 mr1712 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
vg0123522936 NA 4.61E-06 mr1837 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
vg0123522936 NA 1.33E-08 mr1977 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
vg0123522936 NA 9.02E-07 mr1428_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
vg0123522936 NA 1.78E-06 mr1627_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
vg0123522936 9.07E-08 8.57E-10 mr1977_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
vg0123522936 2.24E-06 1.30E-07 mr1977_2 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