\

Search for Variation information by Variation ID:

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

Detailed information for vg0801775699:

Variant ID: vg0801775699 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 1775699
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAAGCATCTTTTGGAAAGTCCAAACCAGTCCCTCAGCTTGGAGAGCAACCAAACCAGGAGATCGAGCCGTTGGTGACCGGGGATGACATGACGATAGAA[G/A]
AATTTGTTATTGACACCGGTCTATCTACGGATCAATTGCTAGGAGTTGAACCAATAGAAAAGGCGGAATTGAAATACATGTATGAACTCGGTAAACCGCT

Reverse complement sequence

AGCGGTTTACCGAGTTCATACATGTATTTCAATTCCGCCTTTTCTATTGGTTCAACTCCTAGCAATTGATCCGTAGATAGACCGGTGTCAATAACAAATT[C/T]
TTCTATCGTCATGTCATCCCCGGTCACCAACGGCTCGATCTCCTGGTTTGGTTGCTCTCCAAGCTGAGGGACTGGTTTGGACTTTCCAAAAGATGCTTTC

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 39.30% 0.10% 17.22% 43.33% NA
All Indica  2759 3.20% 0.20% 27.87% 68.79% NA
All Japonica  1512 98.30% 0.00% 0.26% 1.46% NA
Aus  269 55.40% 0.00% 9.67% 34.94% NA
Indica I  595 3.40% 0.20% 15.13% 81.34% NA
Indica II  465 3.00% 0.60% 15.91% 80.43% NA
Indica III  913 1.60% 0.00% 38.66% 59.69% NA
Indica Intermediate  786 4.80% 0.10% 32.06% 62.98% NA
Temperate Japonica  767 98.20% 0.00% 0.13% 1.69% NA
Tropical Japonica  504 98.80% 0.00% 0.20% 0.99% NA
Japonica Intermediate  241 97.50% 0.00% 0.83% 1.66% NA
VI/Aromatic  96 91.70% 0.00% 2.08% 6.25% NA
Intermediate  90 53.30% 1.10% 14.44% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0801775699 G -> A LOC_Os08g03730.1 missense_variant ; p.Glu679Lys; MODERATE nonsynonymous_codon ; E679K Average:11.153; most accessible tissue: Minghui63 root, score: 21.615 benign 0.917 DELETERIOUS 0.01
vg0801775699 G -> DEL LOC_Os08g03730.1 N frameshift_variant Average:11.153; most accessible tissue: Minghui63 root, score: 21.615 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0801775699 NA 5.71E-10 mr1352 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
vg0801775699 NA 6.77E-06 mr1586 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
vg0801775699 3.78E-07 5.53E-10 mr1739 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
vg0801775699 1.03E-07 1.84E-17 mr1739 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
vg0801775699 NA 8.11E-08 mr1740 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
vg0801775699 NA 1.01E-12 mr1751 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
vg0801775699 NA 1.75E-06 mr1751 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
vg0801775699 NA 7.00E-06 mr1654_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
vg0801775699 NA 1.43E-10 mr1734_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
vg0801775699 1.01E-06 NA mr1739_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
vg0801775699 1.71E-07 2.96E-16 mr1739_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
vg0801775699 NA 2.43E-06 mr1834_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