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Detailed information for vg1203659267:

Variant ID: vg1203659267 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3659267
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.10, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:


TGGGCCTGAGGATGACATCGAGGATCCCTTTGTTGATCTTCCTCCGGAGTACGACTTCTTTGGTGGGTTTGGCCATGGCTACCCTCCTCCTCCACCTCCC[G/A]
AGGATCCACCTCAGGCCCCGTTCGTGTGAGCCATCTTCGCTTCATCCTCTCTTTTTGGTGCTTCGATGCCAAAGGGGGAGAATATCTATCTCTTTTTCAT

Reverse complement sequence

ATGAAAAAGAGATAGATATTCTCCCCCTTTGGCATCGAAGCACCAAAAAGAGAGGATGAAGCGAAGATGGCTCACACGAACGGGGCCTGAGGTGGATCCT[C/T]
GGGAGGTGGAGGAGGAGGGTAGCCATGGCCAAACCCACCAAAGAAGTCGTACTCCGGAGGAAGATCAACAAAGGGATCCTCGATGTCATCCTCAGGCCCA

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 54.30% 45.70% 0.02% 0.00% NA
All Indica  2759 88.10% 11.80% 0.04% 0.00% NA
All Japonica  1512 1.10% 98.90% 0.00% 0.00% NA
Aus  269 32.00% 68.00% 0.00% 0.00% NA
Indica I  595 86.10% 13.90% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 86.90% 13.10% 0.00% 0.00% NA
Indica Intermediate  786 85.60% 14.20% 0.13% 0.00% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 33.30% 66.70% 0.00% 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
vg1203659267 G -> A LOC_Os12g07410.1 missense_variant ; p.Glu304Lys; MODERATE nonsynonymous_codon ; E304K Average:55.346; most accessible tissue: Zhenshan97 young leaf, score: 72.34 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203659267 NA 2.30E-09 mr1379 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
vg1203659267 NA 2.21E-20 mr1580 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
vg1203659267 NA 1.10E-09 mr1714 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
vg1203659267 NA 1.49E-20 mr1627_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
vg1203659267 NA 1.19E-06 mr1931_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