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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0402417093:

Variant ID: vg0402417093 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2417093
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


GCTCGCCGACAATATTGTGGACGTGTATATGCACATGCCTTCAGGGAAGGACATGTGGGATGCTCTTGAGGCCAAGTTCGAGGTTTCCGATGCCGGCAGC[A/G]
AGCTGTATGTCATGGAGCAGTTTTATGACTACAAGATGGTCGATGATCGTTCTGTAGTGGAACAGGCTCATGAGATTCAGATGTTGGCAAAGGAACTTGA

Reverse complement sequence

TCAAGTTCCTTTGCCAACATCTGAATCTCATGAGCCTGTTCCACTACAGAACGATCATCGACCATCTTGTAGTCATAAAACTGCTCCATGACATACAGCT[T/C]
GCTGCCGGCATCGGAAACCTCGAACTTGGCCTCAAGAGCATCCCACATGTCCTTCCCTGAAGGCATGTGCATATACACGTCCACAATATTGTCGGCGAGC

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 15.30% 9.20% 13.50% 62.00% NA
All Indica  2759 3.80% 1.60% 11.92% 82.71% NA
All Japonica  1512 36.10% 24.90% 16.93% 22.09% NA
Aus  269 3.70% 1.50% 7.06% 87.73% NA
Indica I  595 1.20% 0.70% 4.20% 93.95% NA
Indica II  465 1.30% 2.80% 3.01% 92.90% NA
Indica III  913 6.60% 0.90% 20.26% 72.29% NA
Indica Intermediate  786 3.90% 2.40% 13.36% 80.28% NA
Temperate Japonica  767 44.20% 43.90% 3.65% 8.21% NA
Tropical Japonica  504 26.80% 2.20% 27.18% 43.85% NA
Japonica Intermediate  241 29.90% 11.60% 37.76% 20.75% NA
VI/Aromatic  96 45.80% 2.10% 22.92% 29.17% NA
Intermediate  90 18.90% 12.20% 13.33% 55.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402417093 A -> DEL LOC_Os04g04990.1 N frameshift_variant Average:7.605; most accessible tissue: Zhenshan97 root, score: 12.891 N N N N
vg0402417093 A -> G LOC_Os04g04990.1 missense_variant ; p.Lys72Glu; MODERATE nonsynonymous_codon ; K72E Average:7.605; most accessible tissue: Zhenshan97 root, score: 12.891 possibly damaging -1.637 TOLERATED 0.98

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402417093 NA 2.60E-09 mr1137 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
vg0402417093 NA 5.93E-08 mr1164 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
vg0402417093 NA 4.39E-11 mr1182 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
vg0402417093 NA 1.29E-07 mr1182 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
vg0402417093 NA 6.08E-07 mr1282 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
vg0402417093 NA 4.60E-06 mr1503 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
vg0402417093 NA 3.37E-07 mr1650 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
vg0402417093 NA 6.30E-06 mr1658 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
vg0402417093 5.99E-07 NA mr1670 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
vg0402417093 NA 1.50E-06 mr1681 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
vg0402417093 NA 3.92E-08 mr1137_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
vg0402417093 NA 5.90E-06 mr1627_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