Search for Variation information by Variation ID:

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

Detailed information for vg0717367275:

Variant ID: vg0717367275 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17367275
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACACCAGCATCATGGAACGGCAGCGCCAACACGCAATGGGATCAACAAGGCCTCATCAACGCCTTCAACACGGTATCACTGTCCCAACCTCCGTCTAGC[G/A]
ACTGGTATATAGACTCGGGTGCTTCTTCTCACATGACGTCCGATGCCGGTACCCTCTCCTTTTCCTCCCAACCTAACCCTAATACACTGTCTCATATTAT

Reverse complement sequence

ATAATATGAGACAGTGTATTAGGGTTAGGTTGGGAGGAAAAGGAGAGGGTACCGGCATCGGACGTCATGTGAGAAGAAGCACCCGAGTCTATATACCAGT[C/T]
GCTAGACGGAGGTTGGGACAGTGATACCGTGTTGAAGGCGTTGATGAGGCCTTGTTGATCCCATTGCGTGTTGGCGCTGCCGTTCCATGATGCTGGTGTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 3.70% 1.97% 0.00% NA
All Indica  2759 90.40% 6.30% 3.33% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 67.20% 20.80% 11.93% 0.00% NA
Indica II  465 96.80% 1.90% 1.29% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 93.00% 5.10% 1.91% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0717367275 G -> A LOC_Os07g29570.1 missense_variant ; p.Asp564Asn; MODERATE nonsynonymous_codon ; D564N Average:70.497; most accessible tissue: Zhenshan97 young leaf, score: 89.112 benign 0.603 TOLERATED 0.44

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717367275 NA 3.84E-10 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0717367275 NA 1.49E-06 mr1038_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
vg0717367275 NA 9.03E-06 mr1159_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
vg0717367275 2.14E-06 NA mr1378_2 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
vg0717367275 2.92E-07 2.07E-07 mr1378_2 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
vg0717367275 NA 6.37E-06 mr1669_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
vg0717367275 NA 3.35E-06 mr1682_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
vg0717367275 NA 2.06E-06 mr1864_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