Search for Variation information by Variation ID:

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

Detailed information for vg0322796391:

Variant ID: vg0322796391 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22796391
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATCTGGGGTGACACCACAGGAAGAAATACATGGATCAAGCTCAGCACAATGAGCTACGACATGAGCTGCAACATTACATAACCGATTGACATGCACAAA[C/T]
GAACAAAATAAAAAACTAGAAACCATCATGTTGATATCACGGACAACACAACCAACAGAAGAACGATCCCTTGTCAACGATTGTGTAGGATCGAATCACA

Reverse complement sequence

TGTGATTCGATCCTACACAATCGTTGACAAGGGATCGTTCTTCTGTTGGTTGTGTTGTCCGTGATATCAACATGATGGTTTCTAGTTTTTTATTTTGTTC[G/A]
TTTGTGCATGTCAATCGGTTATGTAATGTTGCAGCTCATGTCGTAGCTCATTGTGCTGAGCTTGATCCATGTATTTCTTCCTGTGGTGTCACCCCAGATT

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 98.90% 0.80% 0.23% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 97.20% 2.20% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 94.40% 4.30% 1.30% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0322796391 C -> T LOC_Os03g41000.1 upstream_gene_variant ; 2448.0bp to feature; MODIFIER silent_mutation Average:37.119; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0322796391 C -> T LOC_Os03g41010.1 downstream_gene_variant ; 813.0bp to feature; MODIFIER silent_mutation Average:37.119; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0322796391 C -> T LOC_Os03g41000-LOC_Os03g41010 intergenic_region ; MODIFIER silent_mutation Average:37.119; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322796391 3.97E-08 4.47E-10 mr1210 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
vg0322796391 1.34E-07 1.04E-09 mr1305 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
vg0322796391 5.78E-08 2.49E-11 mr1585 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
vg0322796391 2.48E-07 1.51E-09 mr1586 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
vg0322796391 8.56E-06 1.07E-07 mr1765 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
vg0322796391 6.92E-09 5.82E-10 mr1305_2 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
vg0322796391 7.83E-06 3.12E-06 mr1409_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
vg0322796391 2.57E-06 7.93E-06 mr1559_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
vg0322796391 1.65E-09 1.98E-11 mr1585_2 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