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Detailed information for vg0321444070:

Variant ID: vg0321444070 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21444070
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


GCGCCTCAATACCACCACGGTACCTCGAAAAGGAGCTGTGACAGTACCCCTCGCATAACACAATCCACCACAACGCATTGTTCCTGGATCATAATCACCC[T/C]
CTTATAAACAAGGCATGGACTCCCCAGCGACCCCCGTGGGCTTATCTCCGCCACTTCTCAGTCTGGTGCCCCGCAATGAACCATGTTATACAAAAGGTAA

Reverse complement sequence

TTACCTTTTGTATAACATGGTTCATTGCGGGGCACCAGACTGAGAAGTGGCGGAGATAAGCCCACGGGGGTCGCTGGGGAGTCCATGCCTTGTTTATAAG[A/G]
GGGTGATTATGATCCAGGAACAATGCGTTGTGGTGGATTGTGTTATGCGAGGGGTACTGTCACAGCTCCTTTTCGAGGTACCGTGGTGGTATTGAGGCGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.80% 33.00% 0.00% 0.17% NA
All Indica  2759 98.10% 1.70% 0.00% 0.22% NA
All Japonica  1512 9.00% 91.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 97.20% 2.60% 0.00% 0.22% NA
Indica III  913 98.80% 1.10% 0.00% 0.11% NA
Indica Intermediate  786 97.50% 2.00% 0.00% 0.51% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 9.10% 90.90% 0.00% 0.00% NA
Japonica Intermediate  241 34.00% 66.00% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 48.90% 48.90% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0321444070 T -> C LOC_Os03g38620-LOC_Os03g38640 intergenic_region ; MODIFIER silent_mutation Average:51.038; most accessible tissue: Zhenshan97 flag leaf, score: 73.822 N N N N
vg0321444070 T -> DEL N N silent_mutation Average:51.038; most accessible tissue: Zhenshan97 flag leaf, score: 73.822 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321444070 NA 2.34E-06 mr1278 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
vg0321444070 NA 3.25E-10 mr1307 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
vg0321444070 NA 6.53E-36 mr1670 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
vg0321444070 NA 2.85E-11 mr1713 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
vg0321444070 NA 6.29E-06 mr1718 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
vg0321444070 5.39E-11 6.82E-139 mr1750 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
vg0321444070 NA 7.86E-12 mr1750 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
vg0321444070 NA 4.08E-22 mr1839 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
vg0321444070 NA 4.54E-39 mr1873 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
vg0321444070 NA 1.74E-06 mr1886 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
vg0321444070 NA 3.99E-06 mr1932 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
vg0321444070 NA 1.46E-98 mr1987 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
vg0321444070 3.59E-07 1.12E-166 mr1750_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
vg0321444070 NA 2.07E-14 mr1750_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
vg0321444070 NA 1.80E-10 mr1893_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