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Detailed information for vg0825345627:

Variant ID: vg0825345627 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25345627
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


CATGGCTGAGCATACTCCGCGCCTGTACATCCAAGGGAGCTGCGGGCTTAGGCCAAGGCGTGCACGCCTACATGGAGAAGACGATTGGTCATAGACATGT[C/T]
GCAGTTTGCACATCGCTCATGGATATGTACTCAAAGATAGGCAATGCACGGAGTGCACTCCAGATATTTCAGTGTCTCAAAAGAAAGGATTTGATGGCAT

Reverse complement sequence

ATGCCATCAAATCCTTTCTTTTGAGACACTGAAATATCTGGAGTGCACTCCGTGCATTGCCTATCTTTGAGTACATATCCATGAGCGATGTGCAAACTGC[G/A]
ACATGTCTATGACCAATCGTCTTCTCCATGTAGGCGTGCACGCCTTGGCCTAAGCCCGCAGCTCCCTTGGATGTACAGGCGCGGAGTATGCTCAGCCATG

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 94.90% 5.10% 0.00% 0.00% NA
All Indica  2759 97.90% 2.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 33.80% 66.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 96.20% 3.80% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0825345627 C -> T LOC_Os08g40020.1 synonymous_variant ; p.Val297Val; LOW synonymous_codon Average:77.873; most accessible tissue: Zhenshan97 young leaf, score: 87.993 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825345627 NA 3.74E-06 mr1349 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
vg0825345627 NA 4.91E-20 mr1095_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
vg0825345627 NA 2.03E-12 mr1409_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
vg0825345627 NA 3.03E-16 mr1587_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
vg0825345627 NA 1.25E-12 mr1918_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