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Detailed information for vg0801912932:

Variant ID: vg0801912932 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 1912932
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: Unkown

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAGTATAAATGTGTGGCGATGCGCCGAATTGTATTGATTGTGAGATATTTTACAATGACCCCGGGTGTACATATTTATACCCATGGGGAGATACTAGTC[A/C]
TTGTAGGACAAGAAAGAAACTTTCTTAAAGATAAAAGGAAAATATAAAGTCCTTATAGGACACTAAACACACTTTCCTAAAGATAAAAGGAAACTAACAA

Reverse complement sequence

TTGTTAGTTTCCTTTTATCTTTAGGAAAGTGTGTTTAGTGTCCTATAAGGACTTTATATTTTCCTTTTATCTTTAAGAAAGTTTCTTTCTTGTCCTACAA[T/G]
GACTAGTATCTCCCCATGGGTATAAATATGTACACCCGGGGTCATTGTAAAATATCTCACAATCAATACAATTCGGCGCATCGCCACACATTTATACTTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of Unkown(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.90% 0.00% 5.06% 6.03% NA
All Indica  2759 81.30% 0.00% 8.55% 10.11% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.13% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 72.60% 0.00% 8.74% 18.66% NA
Indica II  465 90.30% 0.00% 3.44% 6.24% NA
Indica III  913 81.10% 0.00% 11.83% 7.12% NA
Indica Intermediate  786 83.00% 0.00% 7.63% 9.41% NA
Temperate Japonica  767 99.90% 0.00% 0.00% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 0.00% 2.22% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0801912932 A -> C LOC_Os08g03990.1 upstream_gene_variant ; 1102.0bp to feature; MODIFIER N Average:59.291; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 N N N N
vg0801912932 A -> C LOC_Os08g03980-LOC_Os08g03990 intergenic_region ; MODIFIER N Average:59.291; most accessible tissue: Zhenshan97 flag leaf, score: 74.162 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0801912932 NA 3.10E-12 mr1739 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
vg0801912932 NA 6.60E-09 mr1739 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
vg0801912932 NA 6.16E-11 mr1739_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
vg0801912932 NA 4.37E-07 mr1899_2 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
vg0801912932 NA 4.62E-06 mr1899_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