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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0524983984:

Variant ID: vg0524983984 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 24983984
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTGCATATTCCTGAACAAGATGCTTCCATAGTTAGTCAATTCAGCATGAAGACGAAATTATGTTCTGATCATAGTTTGAAGATTTCCGATACATACCTG[C/T]
GGAGGCGGATTGAATGCATTATATGGCACGACTGGCAGCTGGTGTGAGTAGCTGACGACGATTGCATTTGAGAAGATTTTATACATCCTCTCCTTCATGA

Reverse complement sequence

TCATGAAGGAGAGGATGTATAAAATCTTCTCAAATGCAATCGTCGTCAGCTACTCACACCAGCTGCCAGTCGTGCCATATAATGCATTCAATCCGCCTCC[G/A]
CAGGTATGTATCGGAAATCTTCAAACTATGATCAGAACATAATTTCGTCTTCATGCTGAATTGACTAACTATGGAAGCATCTTGTTCAGGAATATGCACT

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 40.80% 2.60% 3.55% 53.00% NA
All Indica  2759 10.50% 4.20% 5.58% 79.74% NA
All Japonica  1512 99.10% 0.20% 0.20% 0.53% NA
Aus  269 4.80% 1.50% 1.49% 92.19% NA
Indica I  595 3.70% 4.40% 3.19% 88.74% NA
Indica II  465 25.60% 1.70% 11.40% 61.29% NA
Indica III  913 7.20% 5.80% 4.60% 82.37% NA
Indica Intermediate  786 10.40% 3.70% 5.09% 80.79% NA
Temperate Japonica  767 98.80% 0.40% 0.26% 0.52% NA
Tropical Japonica  504 99.00% 0.00% 0.20% 0.79% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 0.00% 0.00% 11.46% NA
Intermediate  90 50.00% 0.00% 7.78% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0524983984 C -> T LOC_Os05g43020.1 synonymous_variant ; p.Pro294Pro; LOW synonymous_codon Average:5.139; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0524983984 C -> DEL LOC_Os05g43020.1 N frameshift_variant Average:5.139; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0524983984 NA 8.65E-08 mr1162 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
vg0524983984 NA 1.37E-06 mr1352 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
vg0524983984 NA 9.35E-06 mr1415 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
vg0524983984 2.05E-06 2.05E-06 mr1492 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
vg0524983984 NA 9.35E-06 mr1567 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
vg0524983984 NA 1.02E-24 mr1903 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
vg0524983984 NA 1.92E-15 mr1162_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
vg0524983984 NA 9.78E-20 mr1195_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
vg0524983984 NA 9.24E-06 mr1359_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
vg0524983984 NA 1.86E-12 mr1520_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
vg0524983984 NA 4.85E-08 mr1654_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
vg0524983984 NA 1.45E-08 mr1907_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