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Detailed information for vg0208043154:

Variant ID: vg0208043154 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8043154
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGGATGTACAACAATTTCCTCAAGAGCAACCTGCTATTGCTTCTATGCTGAATCAAACAGGTGCTCTAAAAACCTCTATTCCCTTCCCTGATGTGACT[G/A]
ATTTGGATCGATCCCCTTCTGATGTAGCAAATTCTGTTGGTGTGATGGGTTTGGGGGGTAGTGTTCCACCGATGTCTTATCCTCAGTTTGATGGTGTTAA

Reverse complement sequence

TTAACACCATCAAACTGAGGATAAGACATCGGTGGAACACTACCCCCCAAACCCATCACACCAACAGAATTTGCTACATCAGAAGGGGATCGATCCAAAT[C/T]
AGTCACATCAGGGAAGGGAATAGAGGTTTTTAGAGCACCTGTTTGATTCAGCATAGAAGCAATAGCAGGTTGCTCTTGAGGAAATTGTTGTACATCCAAC

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 49.30% 1.80% 1.48% 47.42% NA
All Indica  2759 30.50% 0.00% 2.10% 67.38% NA
All Japonica  1512 92.10% 5.60% 0.40% 1.85% NA
Aus  269 2.20% 0.00% 1.49% 96.28% NA
Indica I  595 36.50% 0.00% 1.68% 61.85% NA
Indica II  465 15.50% 0.00% 2.15% 82.37% NA
Indica III  913 35.50% 0.00% 1.97% 62.54% NA
Indica Intermediate  786 29.10% 0.00% 2.54% 68.32% NA
Temperate Japonica  767 98.30% 0.30% 0.13% 1.30% NA
Tropical Japonica  504 81.00% 15.90% 0.99% 2.18% NA
Japonica Intermediate  241 95.90% 1.20% 0.00% 2.90% NA
VI/Aromatic  96 43.80% 0.00% 0.00% 56.25% NA
Intermediate  90 50.00% 2.20% 2.22% 45.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0208043154 G -> A LOC_Os02g14580.1 missense_variant ; p.Asp326Asn; MODERATE nonsynonymous_codon ; D326N Average:21.899; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 unknown unknown TOLERATED 0.46
vg0208043154 G -> DEL LOC_Os02g14580.1 N frameshift_variant Average:21.899; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208043154 NA 5.03E-07 mr1156 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
vg0208043154 NA 4.72E-06 mr1179 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
vg0208043154 3.13E-06 3.13E-06 mr1264 Jap_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
vg0208043154 NA 1.50E-07 mr1277 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
vg0208043154 NA 1.74E-09 mr1951 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
vg0208043154 NA 5.04E-08 mr1676_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