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Detailed information for vg0209349449:

Variant ID: vg0209349449 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 9349449
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.03, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


CCCCCTGTTGGTTGCGGAAATTCGCCAAGCGACGCTTGTGCGACTCCAATTCTTTGTGCTTGGCTTCCAAGCGGATGCTCTTGTCCACCAGACGTTGGAA[A/G]
TCCGGATAATCCCCGGAGATCAGACGTACGGACAGCTCAGGGTCCATTCCCGCCAAGAACTTCTCTTGCTTTTCCTCATCTTCCCGAACGTCCTCCGGGG

Reverse complement sequence

CCCCGGAGGACGTTCGGGAAGATGAGGAAAAGCAAGAGAAGTTCTTGGCGGGAATGGACCCTGAGCTGTCCGTACGTCTGATCTCCGGGGATTATCCGGA[T/C]
TTCCAACGTCTGGTGGACAAGAGCATCCGCTTGGAAGCCAAGCACAAAGAATTGGAGTCGCACAAGCGTCGCTTGGCGAATTTCCGCAACCAACAGGGGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.60% 2.20% 29.20% 18.98% NA
All Indica  2759 23.80% 2.30% 43.10% 30.77% NA
All Japonica  1512 97.50% 0.10% 0.66% 1.79% NA
Aus  269 24.20% 14.10% 60.97% 0.74% NA
Indica I  595 39.30% 0.00% 28.07% 32.61% NA
Indica II  465 21.70% 8.00% 42.58% 27.74% NA
Indica III  913 12.40% 0.20% 56.19% 31.22% NA
Indica Intermediate  786 26.70% 3.10% 39.57% 30.66% NA
Temperate Japonica  767 98.00% 0.10% 0.13% 1.69% NA
Tropical Japonica  504 96.60% 0.00% 1.19% 2.18% NA
Japonica Intermediate  241 97.50% 0.00% 1.24% 1.24% NA
VI/Aromatic  96 91.70% 0.00% 8.33% 0.00% NA
Intermediate  90 66.70% 2.20% 10.00% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0209349449 A -> G LOC_Os02g16400.1 synonymous_variant ; p.Asp597Asp; LOW synonymous_codon Average:14.162; most accessible tissue: Zhenshan97 young leaf, score: 25.824 N N N N
vg0209349449 A -> DEL LOC_Os02g16400.1 N frameshift_variant Average:14.162; most accessible tissue: Zhenshan97 young leaf, score: 25.824 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0209349449 6.96E-07 6.96E-07 mr1926 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
vg0209349449 NA 4.92E-06 mr1322_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
vg0209349449 NA 1.09E-06 mr1336_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
vg0209349449 NA 2.93E-06 mr1540_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
vg0209349449 NA 1.75E-06 mr1579_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
vg0209349449 NA 4.08E-06 mr1732_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