Search for Variation information by Variation ID:

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

Detailed information for vg0704593347:

Variant ID: vg0704593347 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4593347
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGCAAACTCTTTCAGCCTCTTCCAAACTGAAGTCGTCATGTAATCGTGGATCCATCAAACTATGCACATCTCCCACATGAAGCTTGTTAATTGCTCGC[A/T]
CAGGAAAATAAGCACCATGATAGCTGTTGCTAGCAGATACTTTAGGTGAATTTCTCCTTCCTGATATGATTTCCAATAGTACCATGCCAAAGCTGTAAAC

Reverse complement sequence

GTTTACAGCTTTGGCATGGTACTATTGGAAATCATATCAGGAAGGAGAAATTCACCTAAAGTATCTGCTAGCAACAGCTATCATGGTGCTTATTTTCCTG[T/A]
GCGAGCAATTAACAAGCTTCATGTGGGAGATGTGCATAGTTTGATGGATCCACGATTACATGACGACTTCAGTTTGGAAGAGGCTGAAAGAGTTTGCAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.50% 46.10% 0.00% 0.34% NA
All Indica  2759 88.80% 10.80% 0.00% 0.40% NA
All Japonica  1512 0.40% 99.30% 0.00% 0.26% NA
Aus  269 14.90% 85.10% 0.00% 0.00% NA
Indica I  595 85.70% 13.90% 0.00% 0.34% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 87.00% 12.60% 0.00% 0.44% NA
Indica Intermediate  786 88.40% 10.90% 0.00% 0.64% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.20% 0.00% 0.40% NA
Japonica Intermediate  241 0.40% 98.80% 0.00% 0.83% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 36.70% 62.20% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0704593347 A -> DEL LOC_Os07g08860.1 N frameshift_variant Average:48.761; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N
vg0704593347 A -> T LOC_Os07g08860.1 missense_variant ; p.Val754Glu; MODERATE nonsynonymous_codon ; V754E Average:48.761; most accessible tissue: Zhenshan97 panicle, score: 75.67 benign 0.81 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0704593347 NA 7.90E-24 mr1083 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
vg0704593347 NA 9.99E-07 mr1083 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
vg0704593347 NA 9.66E-06 mr1107 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
vg0704593347 NA 2.81E-11 mr1138 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
vg0704593347 NA 2.80E-21 mr1155 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
vg0704593347 NA 9.43E-11 mr1195 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
vg0704593347 NA 5.63E-31 mr1204 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
vg0704593347 NA 5.02E-06 mr1560 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
vg0704593347 NA 1.26E-28 mr1793 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
vg0704593347 NA 1.33E-10 mr1819 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
vg0704593347 NA 5.10E-06 mr1860 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
vg0704593347 NA 2.14E-06 mr1707_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