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

Detailed information for vg0322467033:

Variant ID: vg0322467033 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22467033
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACACTTATCAGTGACGGGCCGTAATTTAGGCCCGATTGAGATAACATTCCATATCTCAAACGGGCTTGAAGTTGGGGCCCGTCACAGATGACCATCAT[C/T]
CGTGACGTGCAACAACTTAAGGCCCGTCACAGATGACTCATCAGTGACGGGCTATATACTAATCCCCGGTTGACATGACTTAATCACTTAATCTCTATCG

Reverse complement sequence

CGATAGAGATTAAGTGATTAAGTCATGTCAACCGGGGATTAGTATATAGCCCGTCACTGATGAGTCATCTGTGACGGGCCTTAAGTTGTTGCACGTCACG[G/A]
ATGATGGTCATCTGTGACGGGCCCCAACTTCAAGCCCGTTTGAGATATGGAATGTTATCTCAATCGGGCCTAAATTACGGCCCGTCACTGATAAGTGTCA

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 95.30% 4.70% 0.00% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 28.60% 71.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0322467033 C -> T LOC_Os03g40430.1 upstream_gene_variant ; 4100.0bp to feature; MODIFIER silent_mutation Average:42.935; most accessible tissue: Minghui63 root, score: 79.522 N N N N
vg0322467033 C -> T LOC_Os03g40440.1 intron_variant ; MODIFIER silent_mutation Average:42.935; most accessible tissue: Minghui63 root, score: 79.522 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322467033 NA 2.21E-10 mr1471 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
vg0322467033 NA 5.20E-10 mr1722 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
vg0322467033 NA 1.96E-07 mr1735 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
vg0322467033 4.61E-07 NA mr1134_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
vg0322467033 1.07E-06 NA mr1151_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
vg0322467033 8.72E-07 NA mr1248_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
vg0322467033 1.81E-06 NA mr1263_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
vg0322467033 NA 1.10E-11 mr1409_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
vg0322467033 NA 1.62E-16 mr1530_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
vg0322467033 NA 3.93E-06 mr1815_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
vg0322467033 7.00E-06 NA mr1835_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