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Detailed information for vg0600020896:

Variant ID: vg0600020896 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20896
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


TATCTGAGGGTCCACAACTGGTTTTCAACGAGGTGGTTAGTATAGGGATGGCACATAGGACATTAGGGTGGATAGCATAGACGATGTCGGTGTCAAGCGC[G/A]
TCGACTAACCGCGTCGTTAACGTAGGCAGGCGGGCACGACACTGTGGAATGCAGATGGAGAATTCTGTGCAAATTAAAACCTTGATAACTTTGCCTTCCG

Reverse complement sequence

CGGAAGGCAAAGTTATCAAGGTTTTAATTTGCACAGAATTCTCCATCTGCATTCCACAGTGTCGTGCCCGCCTGCCTACGTTAACGACGCGGTTAGTCGA[C/T]
GCGCTTGACACCGACATCGTCTATGCTATCCACCCTAATGTCCTATGTGCCATCCCTATACTAACCACCTCGTTGAAAACCAGTTGTGGACCCTCAGATA

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 69.90% 1.90% 9.88% 18.26% NA
All Indica  2759 57.70% 0.70% 13.34% 28.27% NA
All Japonica  1512 88.60% 4.50% 4.70% 2.18% NA
Aus  269 83.60% 0.00% 4.83% 11.52% NA
Indica I  595 54.30% 0.00% 22.02% 23.70% NA
Indica II  465 55.90% 0.20% 13.55% 30.32% NA
Indica III  913 62.90% 0.70% 6.24% 30.23% NA
Indica Intermediate  786 55.20% 1.70% 14.89% 28.24% NA
Temperate Japonica  767 95.80% 0.40% 3.52% 0.26% NA
Tropical Japonica  504 77.40% 10.90% 6.55% 5.16% NA
Japonica Intermediate  241 89.20% 4.10% 4.56% 2.07% NA
VI/Aromatic  96 84.40% 0.00% 4.17% 11.46% NA
Intermediate  90 75.60% 3.30% 12.22% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0600020896 G -> A LOC_Os06g01040.1 synonymous_variant ; p.Asp399Asp; LOW synonymous_codon Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0600020896 G -> DEL LOC_Os06g01040.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0600020896 1.88E-06 4.05E-06 mr1114 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
vg0600020896 1.34E-06 3.26E-06 mr1117 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
vg0600020896 9.62E-08 6.15E-08 mr1119 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
vg0600020896 4.58E-06 1.54E-06 mr1240 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
vg0600020896 8.16E-07 1.99E-06 mr1247 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
vg0600020896 3.76E-08 1.23E-07 mr1496 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
vg0600020896 1.14E-06 1.72E-08 mr1961 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
vg0600020896 NA 9.59E-06 mr1072_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
vg0600020896 NA 6.24E-06 mr1075_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
vg0600020896 1.22E-07 2.94E-06 mr1117_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
vg0600020896 2.15E-07 2.91E-06 mr1240_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
vg0600020896 2.29E-07 5.75E-06 mr1496_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