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Detailed information for vg0319618333:

Variant ID: vg0319618333 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19618333
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAGGACGACGACGAGGCAGGGCCTTCGCGAAAGCGGATGCGTGGACAAGTGAAGCTTGCCCCCAGCAAGCGAAGAGTTCCTGCTTCATCTGACTCCGAC[G/A]
CTGACGACAAGGATGATGCCGAAGAACGTGACGGCGAGGAGGAAGGAGAGGAAGAGGAGGAGGTGGAGGCTGTGGCTGATAAGGCCGCGAGCGAGGCGGT

Reverse complement sequence

ACCGCCTCGCTCGCGGCCTTATCAGCCACAGCCTCCACCTCCTCCTCTTCCTCTCCTTCCTCCTCGCCGTCACGTTCTTCGGCATCATCCTTGTCGTCAG[C/T]
GTCGGAGTCAGATGAAGCAGGAACTCTTCGCTTGCTGGGGGCAAGCTTCACTTGTCCACGCATCCGCTTTCGCGAAGGCCCTGCCTCGTCGTCGTCCTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.90% 1.40% 0.25% 0.44% NA
All Indica  2759 99.90% 0.00% 0.04% 0.04% NA
All Japonica  1512 93.70% 4.20% 0.73% 1.32% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.00% 0.13% NA
Temperate Japonica  767 97.40% 2.20% 0.39% 0.00% NA
Tropical Japonica  504 96.40% 2.40% 0.99% 0.20% NA
Japonica Intermediate  241 76.30% 14.50% 1.24% 7.88% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0319618333 G -> A LOC_Os03g35380.1 missense_variant ; p.Ala363Thr; MODERATE nonsynonymous_codon ; A363T Average:67.164; most accessible tissue: Zhenshan97 flag leaf, score: 83.994 unknown unknown TOLERATED 0.10
vg0319618333 G -> DEL LOC_Os03g35380.1 N frameshift_variant Average:67.164; most accessible tissue: Zhenshan97 flag leaf, score: 83.994 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319618333 NA 1.29E-06 Grain_weight Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0319618333 6.03E-06 1.65E-06 mr1546_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
vg0319618333 5.90E-06 5.90E-06 mr1914_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