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Detailed information for vg0801775717:

Variant ID: vg0801775717 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 1775717
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCCAAACCAGTCCCTCAGCTTGGAGAGCAACCAAACCAGGAGATCGAGCCGTTGGTGACCGGGGATGACATGACGATAGAAGAATTTGTTATTGACACC[G/A]
GTCTATCTACGGATCAATTGCTAGGAGTTGAACCAATAGAAAAGGCGGAATTGAAATACATGTATGAACTCGGTAAACCGCTTGTCAAGCCCGAGCTGGT

Reverse complement sequence

ACCAGCTCGGGCTTGACAAGCGGTTTACCGAGTTCATACATGTATTTCAATTCCGCCTTTTCTATTGGTTCAACTCCTAGCAATTGATCCGTAGATAGAC[C/T]
GGTGTCAATAACAAATTCTTCTATCGTCATGTCATCCCCGGTCACCAACGGCTCGATCTCCTGGTTTGGTTGCTCTCCAAGCTGAGGGACTGGTTTGGAC

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 39.00% 0.10% 16.69% 44.16% NA
All Indica  2759 3.00% 0.20% 26.60% 70.24% NA
All Japonica  1512 97.90% 0.00% 0.66% 1.46% NA
Aus  269 55.40% 0.00% 10.78% 33.83% NA
Indica I  595 3.50% 0.20% 14.79% 81.51% NA
Indica II  465 2.80% 0.60% 15.05% 81.51% NA
Indica III  913 1.10% 0.00% 35.82% 63.09% NA
Indica Intermediate  786 4.80% 0.10% 31.68% 63.36% NA
Temperate Japonica  767 97.90% 0.00% 0.39% 1.69% NA
Tropical Japonica  504 98.40% 0.00% 0.60% 0.99% NA
Japonica Intermediate  241 96.70% 0.00% 1.66% 1.66% NA
VI/Aromatic  96 91.70% 0.00% 2.08% 6.25% NA
Intermediate  90 50.00% 1.10% 15.56% 33.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0801775717 G -> A LOC_Os08g03730.1 missense_variant ; p.Gly685Ser; MODERATE nonsynonymous_codon ; G685N Average:10.887; most accessible tissue: Minghui63 root, score: 21.615 probably damaging 2.122 DELETERIOUS 0.00
vg0801775717 G -> DEL LOC_Os08g03730.1 N frameshift_variant Average:10.887; 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
vg0801775717 NA 7.45E-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
vg0801775717 4.58E-07 2.95E-11 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
vg0801775717 1.69E-07 1.16E-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
vg0801775717 NA 1.71E-08 mr1172_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
vg0801775717 NA 9.86E-07 mr1472_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
vg0801775717 NA 1.66E-07 mr1483_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
vg0801775717 NA 2.46E-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
vg0801775717 NA 5.95E-06 mr1722_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
vg0801775717 NA 1.08E-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
vg0801775717 NA 1.38E-14 mr1739_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
vg0801775717 NA 1.62E-13 mr1807_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
vg0801775717 NA 6.32E-07 mr1807_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
vg0801775717 NA 1.84E-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