\

Search for Variation information by Variation ID:

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

Detailed information for vg0325763022:

Variant ID: vg0325763022 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 25763022
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTCACCGTCTCCTCCAGGGTAGTCCAACTCGAGGACCTCGTACGCGGCTTCCACCAGCTCAACTTTGACCCTCGAGTATCCTGCTGGAATCGGCCTGCA[A/G]
TGGTAAGTCCCTGAAGGGTCCGTTGGGATGGTCATTCCCAACGCCACCTTCACATGATGAGAGGTTATCTATTAGTGAAACCTAAGCAGCAACTTGCGGA

Reverse complement sequence

TCCGCAAGTTGCTGCTTAGGTTTCACTAATAGATAACCTCTCATCATGTGAAGGTGGCGTTGGGAATGACCATCCCAACGGACCCTTCAGGGACTTACCA[T/C]
TGCAGGCCGATTCCAGCAGGATACTCGAGGGTCAAAGTTGAGCTGGTGGAAGCCGCGTACGAGGTCCTCGAGTTGGACTACCCTGGAGGAGACGGTGAGA

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 85.30% 14.40% 0.00% 0.34% NA
All Indica  2759 96.70% 2.80% 0.00% 0.58% NA
All Japonica  1512 70.40% 29.60% 0.00% 0.00% NA
Aus  269 74.70% 25.30% 0.00% 0.00% NA
Indica I  595 96.10% 1.50% 0.00% 2.35% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.50% 0.40% 0.00% 0.11% NA
Indica Intermediate  786 92.10% 7.80% 0.00% 0.13% NA
Temperate Japonica  767 72.00% 28.00% 0.00% 0.00% NA
Tropical Japonica  504 74.40% 25.60% 0.00% 0.00% NA
Japonica Intermediate  241 57.30% 42.70% 0.00% 0.00% NA
VI/Aromatic  96 27.10% 72.90% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0325763022 A -> DEL LOC_Os03g45650.1 N frameshift_variant Average:61.564; most accessible tissue: Zhenshan97 young leaf, score: 75.397 N N N N
vg0325763022 A -> G LOC_Os03g45650.1 synonymous_variant ; p.His87His; LOW synonymous_codon Average:61.564; most accessible tissue: Zhenshan97 young leaf, score: 75.397 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0325763022 NA 8.83E-06 mr1166 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
vg0325763022 NA 3.96E-07 mr1305 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
vg0325763022 NA 9.42E-06 mr1409 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
vg0325763022 NA 8.42E-07 mr1515 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
vg0325763022 8.91E-06 1.72E-06 mr1586 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
vg0325763022 6.38E-06 5.54E-07 mr1765 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
vg0325763022 3.60E-06 NA mr1305_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