Search for Variation information by Variation ID:

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

Detailed information for vg0421984037:

Variant ID: vg0421984037 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21984037
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGTATAGTTTTACACTATTTACGTTCAATGTTTGACTGTTTATTTTATTTAAAAAAATTTATGATTAGTATTTATTATTATTATTATTATATGATAAAA[C/T]
ATGAATAATACTTTATGTGTGATTAAATATTTTCAATTTTTTCATAATTTTTTTAAATAAGACGGTCAGTCAAATGTTGGGTACGGATATCCACGGCTAC

Reverse complement sequence

GTAGCCGTGGATATCCGTACCCAACATTTGACTGACCGTCTTATTTAAAAAAATTATGAAAAAATTGAAAATATTTAATCACACATAAAGTATTATTCAT[G/A]
TTTTATCATATAATAATAATAATAATAAATACTAATCATAAATTTTTTTAAATAAAATAAACAGTCAAACATTGAACGTAAATAGTGTAAAACTATACTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.70% 12.40% 1.99% 0.00% NA
All Indica  2759 96.90% 2.20% 0.91% 0.00% NA
All Japonica  1512 75.90% 21.30% 2.78% 0.00% NA
Aus  269 33.10% 61.00% 5.95% 0.00% NA
Indica I  595 98.80% 0.00% 1.18% 0.00% NA
Indica II  465 97.20% 2.40% 0.43% 0.00% NA
Indica III  913 96.20% 3.40% 0.44% 0.00% NA
Indica Intermediate  786 96.20% 2.30% 1.53% 0.00% NA
Temperate Japonica  767 97.10% 2.00% 0.91% 0.00% NA
Tropical Japonica  504 38.10% 55.80% 6.15% 0.00% NA
Japonica Intermediate  241 87.60% 10.80% 1.66% 0.00% NA
VI/Aromatic  96 74.00% 20.80% 5.21% 0.00% NA
Intermediate  90 73.30% 20.00% 6.67% 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
vg0421984037 C -> T LOC_Os04g36040-LOC_Os04g36050 intergenic_region ; MODIFIER silent_mutation Average:60.673; most accessible tissue: Minghui63 root, score: 86.792 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421984037 NA 1.51E-07 mr1230 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
vg0421984037 4.22E-06 1.39E-10 mr1321 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
vg0421984037 NA 9.57E-06 mr1331 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
vg0421984037 NA 1.68E-06 mr1422 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
vg0421984037 NA 9.35E-06 mr1444 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
vg0421984037 NA 4.49E-07 mr1621 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
vg0421984037 2.27E-06 3.43E-15 mr1696 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
vg0421984037 NA 7.61E-08 mr1993 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
vg0421984037 NA 1.60E-06 mr1277_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