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Detailed information for vg0825263980:

Variant ID: vg0825263980 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25263980
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTACCACCAACCATCACCACTATTCTATATGCACGGGAATATAGTAGGACTCTTAAGGGTGTGTTTAGTTCACGCAAAAAATGGAAGTTTGGTTGAAATT[A/G]
GAACGATTTGACGAAAAAGTTAGAAGTTTATGTGTGTAGGAAAGTTTTGATGTGATGGAAAAGTTGAAAGTTTAAAGAAAAATTTTAGAACTAAACTCGG

Reverse complement sequence

CCGAGTTTAGTTCTAAAATTTTTCTTTAAACTTTCAACTTTTCCATCACATCAAAACTTTCCTACACACATAAACTTCTAACTTTTTCGTCAAATCGTTC[T/C]
AATTTCAACCAAACTTCCATTTTTTGCGTGAACTAAACACACCCTTAAGAGTCCTACTATATTCCCGTGCATATAGAATAGTGGTGATGGTTGGTGGTAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.00% 13.90% 0.04% 0.00% NA
All Indica  2759 85.80% 14.10% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 6.70% 93.30% 0.00% 0.00% NA
Indica I  595 97.50% 2.40% 0.17% 0.00% NA
Indica II  465 95.70% 4.30% 0.00% 0.00% NA
Indica III  913 78.50% 21.40% 0.11% 0.00% NA
Indica Intermediate  786 79.50% 20.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0825263980 A -> G LOC_Os08g39870.1 intron_variant ; MODIFIER silent_mutation Average:42.121; most accessible tissue: Callus, score: 72.882 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825263980 NA 2.58E-10 Heading_date Ind_All Not 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
vg0825263980 6.96E-13 2.38E-25 mr1874 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
vg0825263980 2.59E-10 2.31E-10 mr1874 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
vg0825263980 1.73E-06 2.14E-26 mr1874_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
vg0825263980 5.46E-08 1.29E-09 mr1874_2 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