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Detailed information for vg1009327768:

Variant ID: vg1009327768 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9327768
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTGCATAGCGGCGAGCGCAGTCGGGGCTGCCGCCGGCTGCGATGGAGTGGCTTGGGGCACCACTAGTTGGCTTGTCGAAAGGATCTCCGCCCTGGTCT[G/A]
GAGTGCCCTTGCCACAGCAGCCGCCTTCGCCACGTCGGCCGCGTTCGGCACTTGCACAGAGGCGGCAGGGGCCGAAGGCGTTTGAGATGGCGCAGATGTG

Reverse complement sequence

CACATCTGCGCCATCTCAAACGCCTTCGGCCCCTGCCGCCTCTGTGCAAGTGCCGAACGCGGCCGACGTGGCGAAGGCGGCTGCTGTGGCAAGGGCACTC[C/T]
AGACCAGGGCGGAGATCCTTTCGACAAGCCAACTAGTGGTGCCCCAAGCCACTCCATCGCAGCCGGCGGCAGCCCCGACTGCGCTCGCCGCTATGCAGGC

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 75.00% 24.70% 0.34% 0.04% NA
All Indica  2759 60.00% 39.30% 0.58% 0.07% NA
All Japonica  1512 96.50% 3.50% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 73.80% 25.70% 0.34% 0.17% NA
Indica II  465 39.80% 58.90% 1.29% 0.00% NA
Indica III  913 64.30% 35.20% 0.44% 0.11% NA
Indica Intermediate  786 56.60% 42.90% 0.51% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 90.70% 9.30% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 0.00% 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
vg1009327768 G -> A LOC_Os10g18360.1 stop_gained ; p.Gln57*; HIGH stop_gained Average:66.783; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg1009327768 G -> DEL LOC_Os10g18360.1 N frameshift_variant Average:66.783; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009327768 2.53E-06 1.09E-10 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
vg1009327768 7.17E-07 3.26E-07 mr1053 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
vg1009327768 2.95E-06 NA mr1070 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
vg1009327768 1.31E-06 9.66E-07 mr1128 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
vg1009327768 6.14E-06 7.07E-06 mr1147 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
vg1009327768 NA 9.77E-11 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
vg1009327768 NA 3.15E-09 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
vg1009327768 NA 3.18E-09 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
vg1009327768 6.10E-07 8.34E-10 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
vg1009327768 5.08E-07 1.10E-07 mr1053_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
vg1009327768 5.28E-07 NA mr1128_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
vg1009327768 1.37E-07 3.20E-07 mr1128_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
vg1009327768 2.01E-06 7.81E-13 mr1147_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
vg1009327768 3.65E-06 3.08E-06 mr1147_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
vg1009327768 1.22E-06 2.38E-08 mr1250_2 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
vg1009327768 1.74E-06 1.74E-06 mr1250_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
vg1009327768 NA 1.55E-06 mr1691_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
vg1009327768 NA 6.96E-06 mr1691_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
vg1009327768 NA 3.31E-09 mr1709_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
vg1009327768 NA 3.79E-09 mr1709_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