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Detailed information for vg0720047684:

Variant ID: vg0720047684 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20047684
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTCAGGTGGAAATTGTGCTGCAAAGATGAAGGTTACAGGAAAGATCCTGTTCCGATGCCTCTTGAACTCCCAATTGAACTTGAGACCAGAAGCTCCCC[C/T]
TGGATATGCTTAAAATGATCCACCTGTTTTTAGTTTATGCTTTCACTAGTTGGTTGAAGAGTTGGAAATGTTGCAGTTGTGAAGATCTTGGTAAAGTTGT

Reverse complement sequence

ACAACTTTACCAAGATCTTCACAACTGCAACATTTCCAACTCTTCAACCAACTAGTGAAAGCATAAACTAAAAACAGGTGGATCATTTTAAGCATATCCA[G/A]
GGGGAGCTTCTGGTCTCAAGTTCAATTGGGAGTTCAAGAGGCATCGGAACAGGATCTTTCCTGTAACCTTCATCTTTGCAGCACAATTTCCACCTGAACT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.80% 15.60% 1.23% 41.43% NA
All Indica  2759 19.20% 9.20% 2.03% 69.55% NA
All Japonica  1512 75.60% 23.80% 0.00% 0.60% NA
Aus  269 97.40% 0.00% 0.00% 2.60% NA
Indica I  595 2.00% 10.10% 0.84% 87.06% NA
Indica II  465 7.50% 15.50% 2.58% 74.41% NA
Indica III  913 35.50% 3.00% 2.74% 58.82% NA
Indica Intermediate  786 20.20% 12.10% 1.78% 65.90% NA
Temperate Japonica  767 96.70% 2.30% 0.00% 0.91% NA
Tropical Japonica  504 43.80% 56.20% 0.00% 0.00% NA
Japonica Intermediate  241 74.70% 24.50% 0.00% 0.83% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 38.90% 33.30% 2.22% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0720047684 C -> DEL LOC_Os07g33550.1 N frameshift_variant Average:17.295; most accessible tissue: Callus, score: 74.478 N N N N
vg0720047684 C -> T LOC_Os07g33550.1 synonymous_variant ; p.Pro474Pro; LOW synonymous_codon Average:17.295; most accessible tissue: Callus, score: 74.478 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720047684 NA 4.78E-32 mr1213 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
vg0720047684 NA 6.98E-09 mr1248 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
vg0720047684 NA 5.58E-06 mr1364 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
vg0720047684 NA 6.88E-07 mr1443 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
vg0720047684 NA 1.94E-10 mr1720 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
vg0720047684 NA 1.58E-09 mr1769 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
vg0720047684 NA 3.39E-06 mr1780 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
vg0720047684 NA 5.85E-16 mr1807 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
vg0720047684 NA 1.24E-06 mr1925 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
vg0720047684 NA 1.05E-10 mr1228_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
vg0720047684 2.08E-06 3.79E-14 mr1364_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
vg0720047684 NA 6.54E-11 mr1364_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
vg0720047684 NA 1.50E-24 mr1422_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
vg0720047684 NA 6.64E-06 mr1460_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
vg0720047684 NA 2.93E-14 mr1583_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
vg0720047684 NA 1.04E-18 mr1807_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