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Detailed information for vg1203838792:

Variant ID: vg1203838792 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3838792
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACTTATACTATGAAACGTAGAGAGGGAGTATCAATTATCTAGCAGTACCATCTAATTTCTAGCTAGTGTGCTTAACCTCTGTTTTTTTGGGCAGATTTC[C/A]
TATATATTTTGTCAAATTAAGAAAATGACATGCTTGCTTGAGTTTAGTTCTAGAAACTTAAAAAGAGATTTTAGATAGCTCCTAACTATAGCTAGTACTA

Reverse complement sequence

TAGTACTAGCTATAGTTAGGAGCTATCTAAAATCTCTTTTTAAGTTTCTAGAACTAAACTCAAGCAAGCATGTCATTTTCTTAATTTGACAAAATATATA[G/T]
GAAATCTGCCCAAAAAAACAGAGGTTAAGCACACTAGCTAGAAATTAGATGGTACTGCTAGATAATTGATACTCCCTCTCTACGTTTCATAGTATAAGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.20% 3.80% 0.00% 0.00% NA
All Indica  2759 96.70% 3.30% 0.00% 0.00% NA
All Japonica  1512 95.20% 4.80% 0.00% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 86.20% 13.80% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 90.10% 9.90% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 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
vg1203838792 C -> A LOC_Os12g07640.1 upstream_gene_variant ; 1945.0bp to feature; MODIFIER silent_mutation Average:49.167; most accessible tissue: Callus, score: 78.32 N N N N
vg1203838792 C -> A LOC_Os12g07630.1 downstream_gene_variant ; 1795.0bp to feature; MODIFIER silent_mutation Average:49.167; most accessible tissue: Callus, score: 78.32 N N N N
vg1203838792 C -> A LOC_Os12g07630-LOC_Os12g07640 intergenic_region ; MODIFIER silent_mutation Average:49.167; most accessible tissue: Callus, score: 78.32 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203838792 8.33E-07 NA mr1404_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