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Detailed information for vg0710323977:

Variant ID: vg0710323977 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10323977
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TCACTCATTAAAACCTCATAATTTGAGCAATCATCATCATTAGGAATAAGAGGTTTTAACCTATCAGATTCAGATTTAAGAGATTCAATGATAAATTCCT[G/A]
TTTTCTATACATCTTCTCACACTTCTTATTTTTTGCACTCAAAATATTAATAGCTTCCTCAAAAGCACTCACCTCATTATCTTCATACTCTGTGTCAGAT

Reverse complement sequence

ATCTGACACAGAGTATGAAGATAATGAGGTGAGTGCTTTTGAGGAAGCTATTAATATTTTGAGTGCAAAAAATAAGAAGTGTGAGAAGATGTATAGAAAA[C/T]
AGGAATTTATCATTGAATCTCTTAAATCTGAATCTGATAGGTTAAAACCTCTTATTCCTAATGATGATGATTGCTCAAATTATGAGGTTTTAATGAGTGA

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 97.10% 1.40% 0.57% 0.87% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.20% 4.40% 0.99% 2.45% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 91.40% 8.60% 0.00% 0.00% NA
Tropical Japonica  504 90.30% 0.00% 2.58% 7.14% NA
Japonica Intermediate  241 98.80% 0.00% 0.83% 0.41% NA
VI/Aromatic  96 84.40% 1.00% 12.50% 2.08% NA
Intermediate  90 96.70% 1.10% 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
vg0710323977 G -> DEL LOC_Os07g17480.1 N frameshift_variant Average:20.402; most accessible tissue: Minghui63 young leaf, score: 36.684 N N N N
vg0710323977 G -> A LOC_Os07g17480.1 stop_gained ; p.Gln39*; HIGH stop_gained Average:20.402; most accessible tissue: Minghui63 young leaf, score: 36.684 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710323977 NA 8.33E-10 mr1028 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
vg0710323977 4.62E-07 4.61E-07 mr1369 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
vg0710323977 NA 1.36E-08 mr1453 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
vg0710323977 NA 3.87E-06 mr1510 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
vg0710323977 NA 2.52E-06 mr1616 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
vg0710323977 NA 1.04E-07 mr1648 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
vg0710323977 NA 3.36E-10 mr1652 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
vg0710323977 NA 5.24E-09 mr1697 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
vg0710323977 NA 3.00E-06 mr1358_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
vg0710323977 NA 4.87E-06 mr1381_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
vg0710323977 NA 7.15E-06 mr1510_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
vg0710323977 NA 3.61E-06 mr1702_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
vg0710323977 NA 7.24E-06 mr1788_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