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Detailed information for vg0321827081:

Variant ID: vg0321827081 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21827081
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


CGGACTGCTGTCGGGTCGGCGGTCAGACCGGCCTGATGGCCCGGTCAGACCGGTCGCATGGTTGCGGTTAGACCGGCCAGAAGGCCTGGTCAGACCGGCC[G/A]
ACTGCGAGGAGCTGGTTTCGGCTTCGGATTTTTTGTTTGAGGATACTCCAACTCCATCTCCAAAAGGTATTGGCACATCATGAGACCCCACTTTGATGGT

Reverse complement sequence

ACCATCAAAGTGGGGTCTCATGATGTGCCAATACCTTTTGGAGATGGAGTTGGAGTATCCTCAAACAAAAAATCCGAAGCCGAAACCAGCTCCTCGCAGT[C/T]
GGCCGGTCTGACCAGGCCTTCTGGCCGGTCTAACCGCAACCATGCGACCGGTCTGACCGGGCCATCAGGCCGGTCTGACCGCCGACCCGACAGCAGTCCG

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 47.00% 40.50% 12.48% 0.02% NA
All Indica  2759 71.00% 9.70% 19.25% 0.04% NA
All Japonica  1512 1.10% 98.40% 0.46% 0.00% NA
Aus  269 78.10% 5.60% 16.36% 0.00% NA
Indica I  595 58.50% 10.30% 31.09% 0.17% NA
Indica II  465 79.60% 6.90% 13.55% 0.00% NA
Indica III  913 77.50% 8.00% 14.46% 0.00% NA
Indica Intermediate  786 67.80% 13.00% 19.21% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 2.80% 95.80% 1.39% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 94.80% 1.04% 0.00% NA
Intermediate  90 32.20% 60.00% 7.78% 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
vg0321827081 G -> A LOC_Os03g39284.1 missense_variant ; p.Ser818Leu; MODERATE nonsynonymous_codon ; S818L Average:24.137; most accessible tissue: Zhenshan97 panicle, score: 59.59 possibly damaging 1.521 TOLERATED 0.09
vg0321827081 G -> DEL LOC_Os03g39284.1 N frameshift_variant Average:24.137; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321827081 3.14E-06 NA mr1358 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