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Detailed information for vg0807177027:

Variant ID: vg0807177027 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 7177027
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


AAGATGAGAAGTTTAAATGGACAGCCGAGTGCGACAGGGGTTTTGAGGAGCTCAAAAAGAAATTAGTATCCGCACCAGTTTTGATTCTGCCCGGCCAGAT[G/A]
AAAGACTTCCAAGTCTATTGCGATGCATCCCGCCACGGACTTGGATGTGTCCTAATGCAAGAGGGCAGAGTGGTTGCATATGCCTCGTGGCAGTTGCGTC

Reverse complement sequence

GACGCAACTGCCACGAGGCATATGCAACCACTCTGCCCTCTTGCATTAGGACACATCCAAGTCCGTGGCGGGATGCATCGCAATAGACTTGGAAGTCTTT[C/T]
ATCTGGCCGGGCAGAATCAAAACTGGTGCGGATACTAATTTCTTTTTGAGCTCCTCAAAACCCCTGTCGCACTCGGCTGTCCATTTAAACTTCTCATCTT

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 64.80% 3.50% 31.15% 0.55% NA
All Indica  2759 41.70% 5.90% 52.12% 0.25% NA
All Japonica  1512 98.00% 0.00% 0.73% 1.26% NA
Aus  269 98.90% 0.70% 0.37% 0.00% NA
Indica I  595 38.00% 2.40% 58.99% 0.67% NA
Indica II  465 62.20% 3.70% 34.19% 0.00% NA
Indica III  913 31.30% 10.10% 58.60% 0.00% NA
Indica Intermediate  786 44.50% 5.10% 50.00% 0.38% NA
Temperate Japonica  767 96.30% 0.00% 1.17% 2.48% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 76.70% 0.00% 23.33% 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
vg0807177027 G -> A LOC_Os08g12190.1 missense_variant ; p.Met553Ile; MODERATE nonsynonymous_codon ; M553I Average:21.667; most accessible tissue: Minghui63 panicle, score: 56.842 benign 1.093 DELETERIOUS 0.02
vg0807177027 G -> DEL LOC_Os08g12190.1 N frameshift_variant Average:21.667; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807177027 4.05E-06 2.16E-06 mr1731 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