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Detailed information for vg0604141656:

Variant ID: vg0604141656 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4141656
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


GATGGACAGAAACAAGATCATATACAGAGCTCAAACATTATATGGAGTTCAATGCCAAGCACTCAACTGCCAAGTGATACCCAAATTCATAATACTCAAA[A/G]
CCAAAGATTGGACAGCGGAAGTTTTAACCATAATATTGGTGCCCATTTGGCTGACCAAACAAATGCAAGTGCGTCAATACTTCCGCAAATGAAGTTTGAC

Reverse complement sequence

GTCAAACTTCATTTGCGGAAGTATTGACGCACTTGCATTTGTTTGGTCAGCCAAATGGGCACCAATATTATGGTTAAAACTTCCGCTGTCCAATCTTTGG[T/C]
TTTGAGTATTATGAATTTGGGTATCACTTGGCAGTTGAGTGCTTGGCATTGAACTCCATATAATGTTTGAGCTCTGTATATGATCTTGTTTCTGTCCATC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.00% 2.20% 2.14% 2.73% NA
All Indica  2759 88.10% 3.60% 3.55% 4.68% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.60% 0.30% 6.55% 0.50% NA
Indica II  465 67.50% 12.00% 4.52% 15.91% NA
Indica III  913 99.70% 0.00% 0.22% 0.11% NA
Indica Intermediate  786 83.60% 5.30% 4.58% 6.49% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 3.30% 3.33% 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
vg0604141656 A -> G LOC_Os06g08440.1 missense_variant ; p.Asn598Ser; MODERATE nonsynonymous_codon Average:64.272; most accessible tissue: Minghui63 flag leaf, score: 83.826 unknown unknown TOLERATED 0.75
vg0604141656 A -> DEL LOC_Os06g08440.1 N frameshift_variant Average:64.272; most accessible tissue: Minghui63 flag leaf, score: 83.826 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604141656 NA 3.02E-07 mr1117 Ind_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
vg0604141656 7.71E-07 7.54E-08 mr1120 Ind_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
vg0604141656 NA 2.39E-06 mr1247_2 Ind_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