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Detailed information for vg0209219211:

Variant ID: vg0209219211 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 9219211
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTCCACGTCCAGGGAATACAAGCTGATTGGTTGCTGGATTGAAATGCTCCATCAACCAGCTGCACAAATCAGGTCTGAGCTTCGAGCACTTGAGATCTA[C/T]
GAGGCCATGGAAGCCAGCCCCCTCTATTAGTCGCTTTTGTTCGCCACTCATATGGGGATACAACTTTATAAGTTTCATAGGTGAAGCCCTGCTACTTTCT

Reverse complement sequence

AGAAAGTAGCAGGGCTTCACCTATGAAACTTATAAAGTTGTATCCCCATATGAGTGGCGAACAAAAGCGACTAATAGAGGGGGCTGGCTTCCATGGCCTC[G/A]
TAGATCTCAAGTGCTCGAAGCTCAGACCTGATTTGTGCAGCTGGTTGATGGAGCATTTCAATCCAGCAACCAATCAGCTTGTATTCCCTGGACGTGGAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.50% 4.80% 0.36% 5.35% NA
All Indica  2759 87.60% 7.90% 0.43% 4.02% NA
All Japonica  1512 99.00% 0.10% 0.00% 0.86% NA
Aus  269 52.00% 0.40% 1.86% 45.72% NA
Indica I  595 80.30% 15.10% 0.34% 4.20% NA
Indica II  465 93.50% 2.40% 0.43% 3.66% NA
Indica III  913 90.40% 7.00% 0.66% 1.97% NA
Indica Intermediate  786 86.40% 6.90% 0.25% 6.49% NA
Temperate Japonica  767 99.00% 0.10% 0.00% 0.91% NA
Tropical Japonica  504 99.00% 0.20% 0.00% 0.79% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 4.40% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0209219211 C -> T LOC_Os02g16220.1 missense_variant ; p.Val211Ile; MODERATE nonsynonymous_codon ; V211I Average:17.45; most accessible tissue: Callus, score: 33.14 benign 1.156 DELETERIOUS 0.00
vg0209219211 C -> DEL LOC_Os02g16220.1 N frameshift_variant Average:17.45; most accessible tissue: Callus, score: 33.14 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0209219211 NA 5.00E-10 mr1201 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
vg0209219211 NA 1.24E-10 mr1201 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
vg0209219211 NA 2.62E-07 mr1219 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
vg0209219211 NA 2.92E-09 mr1219 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
vg0209219211 NA 7.83E-09 mr1274 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
vg0209219211 NA 1.13E-07 mr1274 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
vg0209219211 3.25E-07 7.37E-13 mr1201_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
vg0209219211 9.26E-08 3.17E-13 mr1201_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
vg0209219211 3.46E-06 3.02E-09 mr1219_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
vg0209219211 1.67E-07 3.16E-12 mr1219_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
vg0209219211 NA 4.01E-06 mr1236_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
vg0209219211 NA 6.39E-12 mr1274_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
vg0209219211 NA 1.06E-11 mr1274_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
vg0209219211 NA 1.75E-07 mr1498_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
vg0209219211 NA 5.37E-06 mr1901_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
vg0209219211 NA 1.99E-07 mr1925_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