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Detailed information for vg0620602722:

Variant ID: vg0620602722 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20602722
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTAATTGTTGCAACTTCTTTTTGAGCTGTCTGCTCCTCGGGGCGAATTCTATGAGCCACCTCCTTCAAGAGAGAGCAAAGCAATGGTACACCTCTACT[G/A]
TTGGATGTGTAAGCGGTAGTTGGGAGAAGTTGCGAGACAGATTCTGTCTTTCCTTCTTCCCAGTTACTCGTATTACTGCCCTTCGAGTAGAAATTCTCAG

Reverse complement sequence

CTGAGAATTTCTACTCGAAGGGCAGTAATACGAGTAACTGGGAAGAAGGAAAGACAGAATCTGTCTCGCAACTTCTCCCAACTACCGCTTACACATCCAA[C/T]
AGTAGAGGTGTACCATTGCTTTGCTCTCTCTTGAAGGAGGTGGCTCATAGAATTCGCCCCGAGGAGCAGACAGCTCAAAAAGAAGTTGCAACAATTACTG

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 97.20% 1.50% 0.00% 1.21% NA
All Indica  2759 99.90% 0.00% 0.00% 0.07% NA
All Japonica  1512 91.90% 4.60% 0.00% 3.51% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.00% 0.11% NA
Indica Intermediate  786 99.90% 0.00% 0.00% 0.13% NA
Temperate Japonica  767 94.10% 5.10% 0.00% 0.78% NA
Tropical Japonica  504 98.80% 0.00% 0.00% 1.19% NA
Japonica Intermediate  241 70.50% 12.40% 0.00% 17.01% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0620602722 G -> A LOC_Os06g35340.1 missense_variant ; p.Val56Ile; MODERATE nonsynonymous_codon ; V56I Average:18.866; most accessible tissue: Minghui63 flag leaf, score: 25.154 benign 0.877 TOLERATED 0.11
vg0620602722 G -> DEL LOC_Os06g35340.1 N frameshift_variant Average:18.866; most accessible tissue: Minghui63 flag leaf, score: 25.154 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620602722 2.79E-06 2.79E-06 mr1024_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
vg0620602722 8.74E-07 3.33E-07 mr1037_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
vg0620602722 NA 4.47E-06 mr1291_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
vg0620602722 6.35E-06 6.35E-06 mr1367_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
vg0620602722 NA 1.65E-06 mr1565_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
vg0620602722 NA 8.29E-06 mr1726_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
vg0620602722 NA 2.56E-07 mr1827_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