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Detailed information for vg0812793667:

Variant ID: vg0812793667 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 12793667
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.60, T: 0.40, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


CTGTTAAGGCTGAGATTAAACGTTTATATGATGCTGGTTTTATTCGTCCTTGCCGATATGCTGAGTGGGTTTCTAGCATAGTTCCTGTTATCAAGATAAA[C/T]
GGCAAAGTAAGGGTGTGCATTGATTTCAATGATTTAAACAAGGCTACCCCAAAAGATGAGTATCTGTTGATGGTCGTTATTGACCAATTTCAACCGTCAA

Reverse complement sequence

TTGACGGTTGAAATTGGTCAATAACGACCATCAACAGATACTCATCTTTTGGGGTAGCCTTGTTTAAATCATTGAAATCAATGCACACCCTTACTTTGCC[G/A]
TTTATCTTGATAACAGGAACTATGCTAGAAACCCACTCAGCATATCGGCAAGGACGAATAAAACCAGCATCATATAAACGTTTAATCTCAGCCTTAACAG

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 35.00% 8.90% 5.84% 50.32% NA
All Indica  2759 8.30% 9.70% 7.29% 74.77% NA
All Japonica  1512 84.90% 9.10% 0.20% 5.89% NA
Aus  269 2.20% 1.10% 26.02% 70.63% NA
Indica I  595 15.10% 2.40% 3.03% 79.50% NA
Indica II  465 9.70% 4.90% 8.60% 76.77% NA
Indica III  913 1.50% 17.30% 7.45% 73.71% NA
Indica Intermediate  786 10.10% 9.20% 9.54% 71.25% NA
Temperate Japonica  767 87.00% 8.30% 0.26% 4.43% NA
Tropical Japonica  504 81.90% 12.30% 0.00% 5.75% NA
Japonica Intermediate  241 84.20% 4.60% 0.41% 10.79% NA
VI/Aromatic  96 88.50% 7.30% 1.04% 3.12% NA
Intermediate  90 56.70% 5.60% 1.11% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0812793667 C -> T LOC_Os08g21460.1 synonymous_variant ; p.Asn865Asn; LOW synonymous_codon Average:15.371; most accessible tissue: Callus, score: 30.072 N N N N
vg0812793667 C -> DEL LOC_Os08g21460.1 N frameshift_variant Average:15.371; most accessible tissue: Callus, score: 30.072 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0812793667 NA 5.33E-08 mr1510 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
vg0812793667 NA 4.15E-10 mr1630 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
vg0812793667 NA 9.87E-15 mr1035_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
vg0812793667 1.55E-06 9.61E-20 mr1040_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
vg0812793667 NA 8.25E-08 mr1045_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
vg0812793667 NA 2.12E-06 mr1053_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
vg0812793667 NA 7.38E-06 mr1200_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
vg0812793667 NA 8.32E-06 mr1252_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
vg0812793667 NA 4.31E-08 mr1299_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
vg0812793667 2.17E-06 6.30E-23 mr1362_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
vg0812793667 NA 1.06E-09 mr1379_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
vg0812793667 NA 8.19E-06 mr1405_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
vg0812793667 NA 3.21E-13 mr1537_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
vg0812793667 NA 5.44E-07 mr1559_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
vg0812793667 NA 4.03E-17 mr1592_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
vg0812793667 NA 2.11E-11 mr1595_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
vg0812793667 NA 2.72E-09 mr1600_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
vg0812793667 NA 6.95E-26 mr1617_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
vg0812793667 NA 6.11E-06 mr1617_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
vg0812793667 NA 2.11E-19 mr1637_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
vg0812793667 NA 4.91E-15 mr1713_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
vg0812793667 NA 6.76E-06 mr1713_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
vg0812793667 NA 8.49E-07 mr1727_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
vg0812793667 NA 3.90E-08 mr1783_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
vg0812793667 NA 9.72E-07 mr1785_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
vg0812793667 NA 2.60E-09 mr1804_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
vg0812793667 NA 1.29E-08 mr1837_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
vg0812793667 NA 7.34E-06 mr1982_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