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Detailed information for vg0814602612:

Variant ID: vg0814602612 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 14602612
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

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:


GGGAAAGGTTGCTTCGCCTGGAGGTGGCCGGTGTTGTTTTCCCATGTGAGCCGTGCCAAGCTGACAGTAGCTGATGCCCTGATTGCTAACAGATGGATTA[A/G]
CCGATTACAAGGTGCCTTGTCCAATGAAGCTCTGGGTGAATTCTTCCAACTTTGGGATGAAGTTCGCGACGTGTCACTGCAGCAGATGGCTGACACGATC

Reverse complement sequence

GATCGTGTCAGCCATCTGCTGCAGTGACACGTCGCGAACTTCATCCCAAAGTTGGAAGAATTCACCCAGAGCTTCATTGGACAAGGCACCTTGTAATCGG[T/C]
TAATCCATCTGTTAGCAATCAGGGCATCAGCTACTGTCAGCTTGGCACGGCTCACATGGGAAAACAACACCGGCCACCTCCAGGCGAAGCAACCTTTCCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.20% 5.80% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 82.70% 17.30% 0.00% 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 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 68.30% 31.70% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 6.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0814602612 A -> G LOC_Os08g24190.1 missense_variant ; p.Asn431Ser; MODERATE nonsynonymous_codon Average:41.987; most accessible tissue: Zhenshan97 flower, score: 62.374 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0814602612 1.69E-06 1.45E-07 mr1957_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