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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0716064209:

Variant ID: vg0716064209 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16064209
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCGCGCGGGCTACCTTCCTAGTTTTAATAATAGACCTCCCAGGAACTTATTTCTAAAATGAACCCTTTCGCCACACCATGGTAACCGGCGTGGCCAAT[C/T]
TGAGCTACCGCGCCATTGGTCATGGTGTCGCAAATTAAAGGGTGCCCCGTGGCAGTCGTTGCCATTGACAAGGTTAATTAGTCCCTGACGTGGCACAACT

Reverse complement sequence

AGTTGTGCCACGTCAGGGACTAATTAACCTTGTCAATGGCAACGACTGCCACGGGGCACCCTTTAATTTGCGACACCATGACCAATGGCGCGGTAGCTCA[G/A]
ATTGGCCACGCCGGTTACCATGGTGTGGCGAAAGGGTTCATTTTAGAAATAAGTTCCTGGGAGGTCTATTATTAAAACTAGGAAGGTAGCCCGCGCGAAT

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 87.90% 11.50% 0.59% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 66.00% 32.50% 1.46% 0.00% NA
Aus  269 92.60% 6.30% 1.12% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 85.40% 13.60% 1.04% 0.00% NA
Tropical Japonica  504 30.80% 67.30% 1.98% 0.00% NA
Japonica Intermediate  241 78.00% 20.30% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 12.20% 3.33% 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
vg0716064209 C -> T LOC_Os07g27490-LOC_Os07g27500 intergenic_region ; MODIFIER silent_mutation Average:54.194; most accessible tissue: Zhenshan97 young leaf, score: 65.804 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716064209 2.68E-07 8.66E-09 mr1321 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
vg0716064209 NA 2.40E-07 mr1510 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
vg0716064209 NA 1.75E-07 mr1554 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
vg0716064209 NA 1.52E-10 mr1648 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
vg0716064209 NA 4.57E-07 mr1697 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
vg0716064209 NA 1.23E-06 mr1756 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
vg0716064209 9.52E-07 NA mr1844 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
vg0716064209 1.49E-07 NA mr1844 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
vg0716064209 NA 4.20E-13 mr1900 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
vg0716064209 NA 3.53E-12 mr1905 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
vg0716064209 NA 2.28E-07 mr1696_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