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Detailed information for vg1121617620:

Variant ID: vg1121617620 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21617620
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.52, C: 0.48, others allele: 0.00, population size: 46. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCGAGGGTGCCCTTGCTGGCCAAGATCATCGTATCCAATACTGGAAGATGAAGTTTGAAGTGGCGGAACTCGAGAGAACCATGCTGGCAGTGAAGAAA[G/C]
AGCAGGCTGTGGAAACGCTCCAAGGTCGCGAGGTGTGGTTTAACTCGTACTTGAAGAGTTGCTGCACATCTATGGCCAGGGTCTGTAGAGAACTTCGAGT

Reverse complement sequence

ACTCGAAGTTCTCTACAGACCCTGGCCATAGATGTGCAGCAACTCTTCAAGTACGAGTTAAACCACACCTCGCGACCTTGGAGCGTTTCCACAGCCTGCT[C/G]
TTTCTTCACTGCCAGCATGGTTCTCTCGAGTTCCGCCACTTCAAACTTCATCTTCCAGTATTGGATACGATGATCTTGGCCAGCAAGGGCACCCTCGAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.30% 21.60% 6.05% 10.07% NA
All Indica  2759 54.90% 33.90% 7.32% 3.88% NA
All Japonica  1512 72.90% 3.20% 3.17% 20.70% NA
Aus  269 85.50% 2.60% 9.29% 2.60% NA
Indica I  595 65.40% 13.30% 14.29% 7.06% NA
Indica II  465 37.00% 54.60% 6.02% 2.37% NA
Indica III  913 57.60% 36.00% 4.16% 2.19% NA
Indica Intermediate  786 54.50% 34.70% 6.49% 4.33% NA
Temperate Japonica  767 82.70% 1.30% 3.65% 12.39% NA
Tropical Japonica  504 60.10% 6.30% 3.37% 30.16% NA
Japonica Intermediate  241 68.90% 2.50% 1.24% 27.39% NA
VI/Aromatic  96 44.80% 17.70% 7.29% 30.21% NA
Intermediate  90 58.90% 14.40% 4.44% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1121617620 G -> DEL LOC_Os11g36630.1 N frameshift_variant Average:12.475; most accessible tissue: Minghui63 root, score: 25.504 N N N N
vg1121617620 G -> C LOC_Os11g36630.1 missense_variant ; p.Glu590Gln; MODERATE nonsynonymous_codon ; E590Q Average:12.475; most accessible tissue: Minghui63 root, score: 25.504 benign 1.135 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121617620 1.20E-06 7.78E-11 mr1053 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
vg1121617620 1.70E-08 8.52E-09 mr1053 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
vg1121617620 4.61E-07 1.54E-06 mr1070 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
vg1121617620 9.36E-06 NA mr1128 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
vg1121617620 5.77E-08 4.27E-08 mr1128 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
vg1121617620 6.59E-06 7.04E-06 mr1139 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
vg1121617620 9.39E-06 1.16E-06 mr1145 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
vg1121617620 6.88E-08 9.66E-08 mr1147 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
vg1121617620 NA 3.44E-06 mr1283 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
vg1121617620 4.67E-06 2.12E-06 mr1436 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
vg1121617620 NA 7.27E-07 mr1709 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
vg1121617620 NA 7.74E-07 mr1709 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
vg1121617620 5.31E-06 NA mr1913 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
vg1121617620 NA 1.68E-07 mr1913 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
vg1121617620 NA 1.36E-06 mr1956 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
vg1121617620 NA 5.57E-07 mr1027_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
vg1121617620 NA 5.50E-06 mr1053_2 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