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

Detailed information for vg0210662977:

Variant ID: vg0210662977 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 10662977
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATCATGTGTACCTTCGTGTCACGCCTCTCCGAGGGGTTCATCGTTTCCACACCAAAGGAAAATTGGCACCACGTTTCGTGGGACCTTATAAGATTGTCA[G/A]
TCAAAGAGGTGAGGTTGCTTATCAGTTGGAGTTACCTCAATCCTTGGCAGGTGTTCATAATGTGATCCATGTGTCAAAGTTGAAAAAGTGTTAAAGGGTA

Reverse complement sequence

TACCCTTTAACACTTTTTCAACTTTGACACATGGATCACATTATGAACACCTGCCAAGGATTGAGGTAACTCCAACTGATAAGCAACCTCACCTCTTTGA[C/T]
TGACAATCTTATAAGGTCCCACGAAACGTGGTGCCAATTTTCCTTTGGTGTGGAAACGATGAACCCCTCGGAGAGGCGTGACACGAAGGTACACATGATC

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 91.50% 8.20% 0.25% 0.00% NA
All Indica  2759 85.60% 14.00% 0.40% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 72.80% 26.10% 1.18% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 93.50% 6.40% 0.11% 0.00% NA
Indica Intermediate  786 80.00% 19.60% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 95.60% 3.30% 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
vg0210662977 G -> A LOC_Os02g18340.1 missense_variant ; p.Ser1474Asn; MODERATE nonsynonymous_codon ; S1474N Average:39.672; most accessible tissue: Minghui63 flag leaf, score: 51.386 benign 0.531 DELETERIOUS 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0210662977 NA 3.63E-06 mr1115_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
vg0210662977 NA 1.71E-06 mr1173_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
vg0210662977 3.37E-06 3.37E-06 mr1173_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
vg0210662977 NA 1.31E-06 mr1296_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
vg0210662977 NA 4.42E-06 mr1296_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
vg0210662977 NA 6.19E-07 mr1358_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
vg0210662977 NA 2.29E-06 mr1580_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
vg0210662977 NA 1.82E-06 mr1756_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
vg0210662977 NA 5.64E-06 mr1825_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
vg0210662977 NA 7.45E-06 mr1899_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
vg0210662977 NA 2.97E-07 mr1971_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