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Detailed information for vg0221860877:

Variant ID: vg0221860877 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21860877
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAACAATATCGATGTACGTTTATTGATCTAATCCCTTATGAAAGGTGTTGTCTTGAAATTGTTGTGGTGAAAACCTAACTTTTTGATAGGACAATATG[G/C]
TAAACATATATATATGATATTTTCTTTAGGAAGGTACTATCGCAGTCTCTTGGAGAGTGCCTCGTTTGCATAGATGGCCTTCATGTATTCTCTTTTCATC

Reverse complement sequence

GATGAAAAGAGAATACATGAAGGCCATCTATGCAAACGAGGCACTCTCCAAGAGACTGCGATAGTACCTTCCTAAAGAAAATATCATATATATATGTTTA[C/G]
CATATTGTCCTATCAAAAAGTTAGGTTTTCACCACAACAATTTCAAGACAACACCTTTCATAAGGGATTAGATCAATAAACGTACATCGATATTGTTGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.50% 4.80% 0.68% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 83.10% 14.80% 2.05% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 92.60% 5.20% 2.22% 0.00% NA
Tropical Japonica  504 71.00% 27.00% 1.98% 0.00% NA
Japonica Intermediate  241 78.40% 19.90% 1.66% 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
vg0221860877 G -> C LOC_Os02g36220.1 intron_variant ; MODIFIER silent_mutation Average:43.026; most accessible tissue: Zhenshan97 young leaf, score: 53.969 N N N N
vg0221860877 G -> C LOC_Os02g36220.2 intron_variant ; MODIFIER silent_mutation Average:43.026; most accessible tissue: Zhenshan97 young leaf, score: 53.969 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0221860877 NA 7.37E-06 mr1502 Jap_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
vg0221860877 NA 4.28E-09 mr1543 Jap_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
vg0221860877 6.91E-11 4.22E-16 mr1871 Jap_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
vg0221860877 3.40E-12 1.27E-15 mr1042_2 Jap_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
vg0221860877 9.73E-06 2.13E-08 mr1502_2 Jap_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
vg0221860877 5.53E-07 7.57E-11 mr1543_2 Jap_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
vg0221860877 5.45E-06 1.15E-07 mr1680_2 Jap_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
vg0221860877 4.11E-10 8.77E-15 mr1742_2 Jap_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
vg0221860877 1.08E-18 4.38E-23 mr1871_2 Jap_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