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Detailed information for vg0211628824:

Variant ID: vg0211628824 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11628824
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


AAACTGTCTTTGGTGGGGTCCACTTTGTAACTGACTCCACATTCGATGGATCCACTGCCACACGTTGAGTAGTAATGACGCGACCCAGAAATTTGACTTC[T/C]
GACAACCAGAAGTCACACTTACTGAACTTGGCATATAACTGGTGCTCCTTCAATTTCTTGAGTACCAGACGGAGATGTTGCTCATGTTCTTCTTCAGACT

Reverse complement sequence

AGTCTGAAGAAGAACATGAGCAACATCTCCGTCTGGTACTCAAGAAATTGAAGGAGCACCAGTTATATGCCAAGTTCAGTAAGTGTGACTTCTGGTTGTC[A/G]
GAAGTCAAATTTCTGGGTCGCGTCATTACTACTCAACGTGTGGCAGTGGATCCATCGAATGTGGAGTCAGTTACAAAGTGGACCCCACCAAAGACAGTTT

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 56.90% 36.70% 3.32% 3.09% NA
All Indica  2759 87.10% 3.50% 4.75% 4.71% NA
All Japonica  1512 1.50% 98.10% 0.33% 0.00% NA
Aus  269 84.80% 3.70% 6.32% 5.20% NA
Indica I  595 86.40% 1.50% 7.06% 5.04% NA
Indica II  465 87.30% 3.90% 4.30% 4.52% NA
Indica III  913 89.50% 2.80% 3.29% 4.38% NA
Indica Intermediate  786 84.60% 5.50% 4.96% 4.96% NA
Temperate Japonica  767 0.90% 98.80% 0.26% 0.00% NA
Tropical Japonica  504 2.60% 97.00% 0.40% 0.00% NA
Japonica Intermediate  241 1.20% 98.30% 0.41% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 40.00% 53.30% 4.44% 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
vg0211628824 T -> DEL LOC_Os02g19840.1 N frameshift_variant Average:35.148; most accessible tissue: Minghui63 young leaf, score: 53.016 N N N N
vg0211628824 T -> C LOC_Os02g19840.1 synonymous_variant ; p.Ser559Ser; LOW synonymous_codon Average:35.148; most accessible tissue: Minghui63 young leaf, score: 53.016 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211628824 NA 3.13E-07 mr1162 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
vg0211628824 NA 1.60E-23 mr1548 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
vg0211628824 NA 2.37E-18 mr1566 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
vg0211628824 NA 3.26E-42 mr1645 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
vg0211628824 NA 1.36E-36 mr1647 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
vg0211628824 NA 3.08E-37 mr1682 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
vg0211628824 NA 2.22E-26 mr1686 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
vg0211628824 NA 4.29E-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
vg0211628824 NA 2.58E-22 mr1754 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
vg0211628824 NA 6.85E-14 mr1874 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
vg0211628824 NA 5.96E-09 mr1379_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
vg0211628824 NA 8.60E-16 mr1416_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
vg0211628824 NA 3.08E-18 mr1874_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