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Detailed information for vg0711195681:

Variant ID: vg0711195681 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 11195681
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TTAAGGTTTCGAACTTCTCTTCAAGAGAGAGGTAAGCTTTGTCCAAGCCATCCACTCTCTCTTGAAGTTGAGCGTTCGCCACCTCAAGATTAGCATGAGA[T/C]
TCTTTGGTTTGCTTGTAAAGCCGTACCAAAGCCTCATTTTTCTCTCTCTCCTTAGCAAGTTCACTCTTGAGTTCATGAGACCGCTCTTTCTCATGAATGA

Reverse complement sequence

TCATTCATGAGAAAGAGCGGTCTCATGAACTCAAGAGTGAACTTGCTAAGGAGAGAGAGAAAAATGAGGCTTTGGTACGGCTTTACAAGCAAACCAAAGA[A/G]
TCTCATGCTAATCTTGAGGTGGCGAACGCTCAACTTCAAGAGAGAGTGGATGGCTTGGACAAAGCTTACCTCTCTCTTGAAGAGAAGTTCGAAACCTTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 29.50% 20.10% 9.48% 40.92% NA
All Indica  2759 5.60% 33.30% 14.46% 46.65% NA
All Japonica  1512 75.90% 0.90% 1.46% 21.76% NA
Aus  269 18.60% 2.60% 3.72% 75.09% NA
Indica I  595 7.40% 27.10% 24.87% 40.67% NA
Indica II  465 6.50% 34.00% 11.40% 48.17% NA
Indica III  913 3.60% 36.90% 6.68% 52.79% NA
Indica Intermediate  786 6.10% 33.30% 17.43% 43.13% NA
Temperate Japonica  767 67.90% 0.90% 2.35% 28.81% NA
Tropical Japonica  504 86.10% 0.40% 0.20% 13.29% NA
Japonica Intermediate  241 79.70% 2.10% 1.24% 17.01% NA
VI/Aromatic  96 2.10% 0.00% 6.25% 91.67% NA
Intermediate  90 42.20% 14.40% 12.22% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0711195681 T -> DEL LOC_Os07g18890.1 N frameshift_variant Average:8.091; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N
vg0711195681 T -> C LOC_Os07g18890.1 synonymous_variant ; p.Glu464Glu; LOW synonymous_codon Average:8.091; most accessible tissue: Minghui63 panicle, score: 16.27 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0711195681 7.54E-06 NA mr1089_2 Ind_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
vg0711195681 1.57E-06 9.97E-06 mr1255_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
vg0711195681 NA 5.24E-06 mr1574_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
vg0711195681 NA 4.87E-07 mr1604_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
vg0711195681 4.89E-06 NA mr1679_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
vg0711195681 2.20E-06 NA mr1691_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
vg0711195681 NA 3.43E-11 mr1714_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
vg0711195681 NA 4.59E-15 mr1726_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
vg0711195681 NA 7.28E-08 mr1765_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
vg0711195681 NA 4.53E-08 mr1940_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
vg0711195681 NA 8.15E-15 mr1950_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
vg0711195681 NA 3.63E-12 mr1986_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