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Detailed information for vg0813207586:

Variant ID: vg0813207586 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 13207586
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGAGGAATGTCGTAGAGCATTTGTCCCAGGTATTGACAGCAGCAAGGTTGGCATAGAACCACTGCTTCGCTCTCCCGAGAAGGAGAACGGAAACAGTCG[C/T]
AGCCTGACGGCGTCGGGACTGACACCCTTGATGGTGTACGTGCTACAGATCTCTAGGAACTGTTGCAGATGAGCATTGGCATCCTCATCAGGCTTGCCAC

Reverse complement sequence

GTGGCAAGCCTGATGAGGATGCCAATGCTCATCTGCAACAGTTCCTAGAGATCTGTAGCACGTACACCATCAAGGGTGTCAGTCCCGACGCCGTCAGGCT[G/A]
CGACTGTTTCCGTTCTCCTTCTCGGGAGAGCGAAGCAGTGGTTCTATGCCAACCTTGCTGCTGTCAATACCTGGGACAAATGCTCTACGACATTCCTCTC

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 70.10% 3.80% 5.37% 20.69% NA
All Indica  2759 61.80% 5.40% 6.71% 26.17% NA
All Japonica  1512 82.60% 1.80% 3.17% 12.43% NA
Aus  269 91.40% 1.10% 3.35% 4.09% NA
Indica I  595 44.00% 3.00% 6.05% 46.89% NA
Indica II  465 55.70% 4.10% 5.81% 34.41% NA
Indica III  913 76.80% 9.50% 8.11% 5.59% NA
Indica Intermediate  786 61.30% 3.10% 6.11% 29.52% NA
Temperate Japonica  767 89.80% 0.00% 0.26% 9.91% NA
Tropical Japonica  504 77.20% 2.20% 4.76% 15.87% NA
Japonica Intermediate  241 71.00% 6.60% 9.13% 13.28% NA
VI/Aromatic  96 55.20% 1.00% 8.33% 35.42% NA
Intermediate  90 68.90% 1.10% 4.44% 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
vg0813207586 C -> T LOC_Os08g22006.1 synonymous_variant ; p.Leu41Leu; LOW synonymous_codon Average:7.344; most accessible tissue: Minghui63 young leaf, score: 11.521 N N N N
vg0813207586 C -> DEL LOC_Os08g22006.1 N frameshift_variant Average:7.344; most accessible tissue: Minghui63 young leaf, score: 11.521 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0813207586 NA 1.05E-06 mr1321 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
vg0813207586 NA 6.39E-16 mr1484 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
vg0813207586 NA 6.91E-06 mr1484 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
vg0813207586 6.40E-06 7.93E-14 mr1609 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
vg0813207586 1.24E-07 1.14E-07 mr1609 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
vg0813207586 NA 3.55E-07 mr1716 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
vg0813207586 NA 8.47E-07 mr1717 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
vg0813207586 NA 7.65E-25 mr1841 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
vg0813207586 NA 8.06E-07 mr1841 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
vg0813207586 NA 7.35E-13 mr1883 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
vg0813207586 2.78E-07 2.78E-07 mr1900 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