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Detailed information for vg0126439651:

Variant ID: vg0126439651 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 26439651
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAATTATCAGTTTGCTGCAACATTAGCGATATATTTCAGTTTGCTGCAACATTAGCGACATATTTCAGTTTGCTACAACATTAGAGTGGGAAATTATCA[C/T]
AAAACATAACGTAAAAGTTGCAGTTTTGTGATAATTTCCCACGCTATTGTTGTAGCAAACCGAAACATGTCGCTAATGTTGCAGCAAACTAATAATTTTG

Reverse complement sequence

CAAAATTATTAGTTTGCTGCAACATTAGCGACATGTTTCGGTTTGCTACAACAATAGCGTGGGAAATTATCACAAAACTGCAACTTTTACGTTATGTTTT[G/A]
TGATAATTTCCCACTCTAATGTTGTAGCAAACTGAAATATGTCGCTAATGTTGCAGCAAACTGAAATATATCGCTAATGTTGCAGCAAACTGATAATTTT

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 92.90% 7.10% 0.06% 0.00% NA
All Indica  2759 95.60% 4.40% 0.00% 0.00% NA
All Japonica  1512 87.60% 12.20% 0.20% 0.00% NA
Aus  269 95.20% 4.80% 0.00% 0.00% NA
Indica I  595 94.50% 5.50% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 95.50% 4.50% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 5.00% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 67.10% 32.50% 0.40% 0.00% NA
Japonica Intermediate  241 92.10% 7.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0126439651 C -> T LOC_Os01g46470-LOC_Os01g46490 intergenic_region ; MODIFIER silent_mutation Average:44.689; most accessible tissue: Zhenshan97 flower, score: 71.992 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0126439651 NA 7.54E-06 mr1155 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
vg0126439651 NA 6.28E-08 mr1206 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
vg0126439651 NA 2.45E-08 mr1206 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
vg0126439651 7.10E-06 7.09E-06 mr1208 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
vg0126439651 NA 2.13E-07 mr1229 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
vg0126439651 NA 2.45E-07 mr1229 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
vg0126439651 4.23E-06 NA mr1560 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
vg0126439651 4.26E-07 9.46E-10 mr1596 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
vg0126439651 NA 9.78E-08 mr1596 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
vg0126439651 NA 3.73E-07 mr1668 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
vg0126439651 NA 1.90E-14 mr1410_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