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Detailed information for vg0801635294:

Variant ID: vg0801635294 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 1635294
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGATGAGGGAGCACCGCGCGCCGCGGATCGCCGTCGACGACATGGAGCCGGAGGTGTTCGACGCGCTCCTCCGCTTCGTCTACAGCGACACGCTGGCGCT[C/T]
CCCGGCGACCTCGGGGAAGGCGAGTACAAGGAGATGGTGCGGCAGCTGCTGGAGGCGGCCGACCGGTACGCCATGGACAGGCTCAGGGTGATCTGCGAGC

Reverse complement sequence

GCTCGCAGATCACCCTGAGCCTGTCCATGGCGTACCGGTCGGCCGCCTCCAGCAGCTGCCGCACCATCTCCTTGTACTCGCCTTCCCCGAGGTCGCCGGG[G/A]
AGCGCCAGCGTGTCGCTGTAGACGAAGCGGAGGAGCGCGTCGAACACCTCCGGCTCCATGTCGTCGACGGCGATCCGCGGCGCGCGGTGCTCCCTCATCG

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 58.00% 41.20% 0.08% 0.76% NA
All Indica  2759 94.20% 4.40% 0.07% 1.30% NA
All Japonica  1512 2.40% 97.50% 0.07% 0.00% NA
Aus  269 19.30% 80.70% 0.00% 0.00% NA
Indica I  595 96.00% 1.30% 0.17% 2.52% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 92.80% 6.40% 0.11% 0.77% NA
Indica Intermediate  786 92.20% 6.00% 0.00% 1.78% NA
Temperate Japonica  767 3.00% 96.90% 0.13% 0.00% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 47.80% 51.10% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0801635294 C -> T LOC_Os08g03490.1 synonymous_variant ; p.Leu264Leu; LOW synonymous_codon Average:77.635; most accessible tissue: Zhenshan97 root, score: 83.751 N N N N
vg0801635294 C -> DEL LOC_Os08g03490.1 N frameshift_variant Average:77.635; most accessible tissue: Zhenshan97 root, score: 83.751 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0801635294 NA 4.72E-21 mr1003 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
vg0801635294 NA 1.10E-47 mr1109 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
vg0801635294 NA 1.18E-30 mr1224 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
vg0801635294 NA 1.00E-30 mr1745 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
vg0801635294 NA 6.02E-29 mr1793 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
vg0801635294 NA 1.28E-34 mr1828 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
vg0801635294 NA 2.37E-23 mr1862 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
vg0801635294 NA 1.77E-74 mr1088_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
vg0801635294 NA 2.20E-56 mr1109_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
vg0801635294 NA 3.73E-18 mr1131_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
vg0801635294 NA 1.13E-38 mr1208_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
vg0801635294 NA 1.70E-36 mr1224_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
vg0801635294 NA 4.46E-75 mr1246_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
vg0801635294 NA 7.33E-28 mr1270_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
vg0801635294 NA 3.78E-23 mr1316_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
vg0801635294 NA 9.88E-45 mr1745_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
vg0801635294 NA 1.63E-45 mr1793_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
vg0801635294 NA 3.26E-31 mr1932_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
vg0801635294 NA 2.17E-98 mr1973_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