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Detailed information for vg0615048731:

Variant ID: vg0615048731 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 15048731
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: 74. )

Flanking Sequence (100 bp) in Reference Genome:


GACTATTCCTACCTCGTTTTTTGTCATCGATGGGAAGGGTTCTTACAGCTTGTTGCTTGGAAGGGATTGGATTCACGCCAATTGTTGCATTCCTTCAACT[A/G]
TGCATCAATGTTTGATTCAGTGGCAAGGCGACAAGATAGAGATCGTTCCAGCCGACAGGTCAGTTAATGTTGCCAGTGCCGATTTAGCTCTTTGGGAGAT

Reverse complement sequence

ATCTCCCAAAGAGCTAAATCGGCACTGGCAACATTAACTGACCTGTCGGCTGGAACGATCTCTATCTTGTCGCCTTGCCACTGAATCAAACATTGATGCA[T/C]
AGTTGAAGGAATGCAACAATTGGCGTGAATCCAATCCCTTCCAAGCAACAAGCTGTAAGAACCCTTCCCATCGATGACAAAAAACGAGGTAGGAATAGTC

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 90.40% 8.00% 0.70% 0.89% NA
All Indica  2759 86.10% 13.00% 0.87% 0.07% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.20% 0.50% 0.17% NA
Indica II  465 87.30% 11.80% 0.86% 0.00% NA
Indica III  913 75.40% 24.30% 0.33% 0.00% NA
Indica Intermediate  786 87.90% 10.20% 1.78% 0.13% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 50.00% 0.00% 9.38% 40.62% NA
Intermediate  90 87.80% 11.10% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0615048731 A -> G LOC_Os06g25760.1 missense_variant ; p.Met728Val; MODERATE nonsynonymous_codon ; M728V Average:30.85; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 benign 0.88 TOLERATED 0.10
vg0615048731 A -> DEL LOC_Os06g25760.1 N frameshift_variant Average:30.85; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0615048731 5.64E-07 NA mr1068 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
vg0615048731 4.85E-07 1.01E-08 mr1090 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
vg0615048731 5.09E-06 NA mr1111 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
vg0615048731 1.58E-08 2.07E-10 mr1121 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
vg0615048731 NA 4.12E-06 mr1122 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
vg0615048731 4.85E-06 NA mr1144 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
vg0615048731 2.45E-07 8.24E-10 mr1211 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
vg0615048731 9.82E-06 NA mr1065_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
vg0615048731 4.49E-10 NA mr1068_2 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
vg0615048731 2.50E-06 NA mr1087_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
vg0615048731 1.09E-10 2.88E-09 mr1090_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
vg0615048731 6.95E-06 NA mr1096_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
vg0615048731 1.95E-07 NA mr1111_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
vg0615048731 7.38E-10 7.44E-10 mr1121_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
vg0615048731 5.12E-07 NA mr1144_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
vg0615048731 5.94E-09 NA mr1200_2 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
vg0615048731 9.63E-10 1.08E-10 mr1211_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
vg0615048731 NA 1.26E-07 mr1632_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