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Detailed information for vg0411929663:

Variant ID: vg0411929663 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 11929663
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGCGCACGACGGCGGGCAGCGGTGGACGACAACGGCGGCCATCCCCCGCTTTGGTCCACGCGGATCTAGCGAAAGAGCACAGCGGACGGCGAGCGGATC[C/T]
AGCGAGGGCATGTGGCAGGCGGACAGGCCTTGCCCGGATCCGGCAACAGGGTTCACAGTTCCGACGAAAACCAGTCGAATTCCGAGAAATTTTGAGGTTT

Reverse complement sequence

AAACCTCAAAATTTCTCGGAATTCGACTGGTTTTCGTCGGAACTGTGAACCCTGTTGCCGGATCCGGGCAAGGCCTGTCCGCCTGCCACATGCCCTCGCT[G/A]
GATCCGCTCGCCGTCCGCTGTGCTCTTTCGCTAGATCCGCGTGGACCAAAGCGGGGGATGGCCGCCGTTGTCGTCCACCGCTGCCCGCCGTCGTGCGCCC

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 94.40% 5.60% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 88.40% 11.60% 0.00% 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 99.80% 0.20% 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 92.20% 7.80% 0.00% 0.00% NA
Tropical Japonica  504 90.90% 9.10% 0.00% 0.00% NA
Japonica Intermediate  241 71.40% 28.60% 0.00% 0.00% NA
VI/Aromatic  96 22.90% 77.10% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0411929663 C -> T LOC_Os04g21180.1 upstream_gene_variant ; 4135.0bp to feature; MODIFIER silent_mutation Average:54.21; most accessible tissue: Zhenshan97 young leaf, score: 71.923 N N N N
vg0411929663 C -> T LOC_Os04g21180-LOC_Os04g21190 intergenic_region ; MODIFIER silent_mutation Average:54.21; most accessible tissue: Zhenshan97 young leaf, score: 71.923 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0411929663 1.21E-07 4.38E-09 mr1343 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
vg0411929663 7.36E-08 5.02E-12 mr1829 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
vg0411929663 2.28E-07 NA mr1842 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
vg0411929663 NA 5.06E-06 mr1549_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
vg0411929663 2.08E-07 3.77E-13 mr1829_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
vg0411929663 3.11E-07 2.53E-16 mr1842_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
vg0411929663 4.67E-06 NA mr1933_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