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Detailed information for vg1207399200:

Variant ID: vg1207399200 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 7399200
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, A: 0.11, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTAAAACGGTATTATATGCGCAATTGACCGAAAAACCTTCAGATTTTCTAAAATCGTCCTGATCCAGTTTGTTCCGGACTTTTTTTTCCAAAATAAAC[C/A]
GTTCAGCTTCATTCTATGCGCGGTGGACTGAAAAACCATGATTTTTAAAATCGACCCGGTCGAGACGGTCCTCGACTTAATATTTTTCTGTCCAAAATAA

Reverse complement sequence

TTATTTTGGACAGAAAAATATTAAGTCGAGGACCGTCTCGACCGGGTCGATTTTAAAAATCATGGTTTTTCAGTCCACCGCGCATAGAATGAAGCTGAAC[G/T]
GTTTATTTTGGAAAAAAAAGTCCGGAACAAACTGGATCAGGACGATTTTAGAAAATCTGAAGGTTTTTCGGTCAATTGCGCATATAATACCGTTTTAGGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.50% 39.40% 0.13% 0.00% NA
All Indica  2759 44.80% 55.00% 0.22% 0.00% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 11.20% 88.80% 0.00% 0.00% NA
Indica I  595 68.60% 31.10% 0.34% 0.00% NA
Indica II  465 54.80% 45.20% 0.00% 0.00% NA
Indica III  913 27.80% 72.10% 0.11% 0.00% NA
Indica Intermediate  786 40.60% 59.00% 0.38% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 31.20% 68.80% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg1207399200 C -> A LOC_Os12g13290-LOC_Os12g13295 intergenic_region ; MODIFIER silent_mutation Average:74.897; most accessible tissue: Callus, score: 87.335 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1207399200 NA 1.60E-06 mr1425 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
vg1207399200 NA 1.92E-06 mr1265_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
vg1207399200 NA 2.78E-06 mr1296_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
vg1207399200 NA 3.28E-07 mr1452_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
vg1207399200 NA 4.61E-06 mr1452_2 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
vg1207399200 NA 6.21E-06 mr1454_2 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
vg1207399200 NA 7.60E-08 mr1539_2 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
vg1207399200 NA 4.68E-08 mr1540_2 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
vg1207399200 NA 8.21E-12 mr1576_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
vg1207399200 3.86E-06 3.17E-08 mr1576_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
vg1207399200 NA 8.32E-09 mr1582_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
vg1207399200 NA 8.99E-09 mr1582_2 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
vg1207399200 NA 4.05E-08 mr1732_2 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
vg1207399200 NA 1.69E-08 mr1749_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
vg1207399200 NA 1.33E-08 mr1821_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
vg1207399200 NA 6.71E-06 mr1864_2 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
vg1207399200 NA 7.55E-09 mr1882_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