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Detailed information for vg0624467444:

Variant ID: vg0624467444 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 24467444
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCAGTCGCGCTAAGCGCTTCCCAAAAACATTATTGCCGCCTTCTCCCGGTGCAGGACGTCGAAGGTAGAGGTTCCGGAGACCTGCTCTCCCGATCGCCG[A/G]
TGCACGCCGGCGAGCGGGATGGAGTAATCTATGAGCGACGGCGCAGCACAGAGTAGGAGGCAAACCCTAGATTGATTTTTTCGTGTGTTGCGTGAAGACG

Reverse complement sequence

CGTCTTCACGCAACACACGAAAAAATCAATCTAGGGTTTGCCTCCTACTCTGTGCTGCGCCGTCGCTCATAGATTACTCCATCCCGCTCGCCGGCGTGCA[T/C]
CGGCGATCGGGAGAGCAGGTCTCCGGAACCTCTACCTTCGACGTCCTGCACCGGGAGAAGGCGGCAATAATGTTTTTGGGAAGCGCTTAGCGCGACTGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.10% 10.90% 0.04% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 66.80% 33.10% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 45.50% 54.20% 0.26% 0.00% NA
Tropical Japonica  504 93.80% 6.20% 0.00% 0.00% NA
Japonica Intermediate  241 78.00% 22.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 0.00% 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
vg0624467444 A -> G LOC_Os06g40970.1 downstream_gene_variant ; 3528.0bp to feature; MODIFIER silent_mutation Average:39.588; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0624467444 A -> G LOC_Os06g40980.1 downstream_gene_variant ; 1201.0bp to feature; MODIFIER silent_mutation Average:39.588; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0624467444 A -> G LOC_Os06g40970-LOC_Os06g40980 intergenic_region ; MODIFIER silent_mutation Average:39.588; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0624467444 3.95E-07 NA Yield All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0624467444 NA 2.85E-07 mr1617 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
vg0624467444 NA 2.03E-10 mr1712 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
vg0624467444 NA 4.09E-07 mr1763 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
vg0624467444 NA 1.30E-07 mr1946 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
vg0624467444 NA 1.44E-08 mr1977 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
vg0624467444 NA 4.21E-07 mr1229_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
vg0624467444 NA 5.81E-07 mr1570_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
vg0624467444 NA 5.56E-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
vg0624467444 NA 4.34E-06 mr1763_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
vg0624467444 NA 4.70E-07 mr1880_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