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Detailed information for vg0727490819:

Variant ID: vg0727490819 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27490819
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


ACCAGATGATGGACGCACTGTCAATTGTAGAATTGACGCCCTCAAGGGCTGAGAATTACATGGTTTTCTTGGGTGACACAGGTTTCATGGAATGTAACAC[A/G]
CCTCTCTCTGCCCTAGCGGACAGGGCAAAAGAACTGATGGGTCGTCAGTGGCTGCAAGGCATCAACAGTGCCAACTGAAAAAAAATAAAATGATTTTGCA

Reverse complement sequence

TGCAAAATCATTTTATTTTTTTTCAGTTGGCACTGTTGATGCCTTGCAGCCACTGACGACCCATCAGTTCTTTTGCCCTGTCCGCTAGGGCAGAGAGAGG[T/C]
GTGTTACATTCCATGAAACCTGTGTCACCCAAGAAAACCATGTAATTCTCAGCCCTTGAGGGCGTCAATTCTACAATTGACAGTGCGTCCATCATCTGGT

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 89.70% 5.70% 2.60% 1.97% NA
All Indica  2759 96.00% 0.40% 2.72% 0.94% NA
All Japonica  1512 81.60% 16.20% 1.85% 0.33% NA
Aus  269 69.10% 1.10% 7.43% 22.30% NA
Indica I  595 95.50% 0.20% 4.37% 0.00% NA
Indica II  465 94.60% 0.40% 3.66% 1.29% NA
Indica III  913 98.20% 0.10% 1.10% 0.55% NA
Indica Intermediate  786 94.50% 0.80% 2.80% 1.91% NA
Temperate Japonica  767 98.60% 0.40% 1.04% 0.00% NA
Tropical Japonica  504 53.40% 42.90% 2.98% 0.79% NA
Japonica Intermediate  241 86.70% 10.80% 2.07% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 13.30% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0727490819 A -> DEL LOC_Os07g46060.1 N frameshift_variant Average:19.822; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg0727490819 A -> G LOC_Os07g46060.1 synonymous_variant ; p.Thr1097Thr; LOW synonymous_codon Average:19.822; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727490819 NA 9.18E-06 mr1213 Jap_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
vg0727490819 NA 1.17E-06 mr1277 Jap_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
vg0727490819 2.22E-06 1.33E-15 mr1871 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
vg0727490819 NA 2.25E-07 mr1871 Jap_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
vg0727490819 1.00E-06 NA mr1517_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
vg0727490819 9.93E-06 NA mr1538_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
vg0727490819 NA 1.74E-07 mr1671_2 Jap_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
vg0727490819 NA 5.40E-09 mr1905_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