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Detailed information for vg0222556989:

Variant ID: vg0222556989 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22556989
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCAACTCTCAGTTTGTTTTTTTTTTTGAAAACTCATAAATTTATTCATATAGTGAGGATTACAGACAGAGCTCAAAGGAAATGGCATCCCCAGAACATC[G/A]
CCATAAAAGATAAGACATAAAAAACAACACCATCCATTCAGAAGGTAAAGCTAGCTGAACTAAGAAAAACATCCTCCAAGATAATCCAAACAGCAGTAAA

Reverse complement sequence

TTTACTGCTGTTTGGATTATCTTGGAGGATGTTTTTCTTAGTTCAGCTAGCTTTACCTTCTGAATGGATGGTGTTGTTTTTTATGTCTTATCTTTTATGG[C/T]
GATGTTCTGGGGATGCCATTTCCTTTGAGCTCTGTCTGTAATCCTCACTATATGAATAAATTTATGAGTTTTCAAAAAAAAAAACAAACTGAGAGTTGAG

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 52.90% 6.30% 20.21% 20.57% NA
All Indica  2759 22.70% 10.30% 33.60% 33.42% NA
All Japonica  1512 97.00% 0.00% 0.73% 2.31% NA
Aus  269 90.70% 3.30% 3.72% 2.23% NA
Indica I  595 26.20% 5.00% 35.29% 33.45% NA
Indica II  465 6.20% 16.80% 39.78% 37.20% NA
Indica III  913 30.00% 8.80% 28.15% 33.08% NA
Indica Intermediate  786 21.20% 12.20% 34.99% 31.55% NA
Temperate Japonica  767 99.50% 0.00% 0.26% 0.26% NA
Tropical Japonica  504 92.10% 0.00% 1.59% 6.35% NA
Japonica Intermediate  241 99.20% 0.00% 0.41% 0.41% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 78.90% 3.30% 7.78% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0222556989 G -> A LOC_Os02g37309.1 stop_gained ; p.Arg250*; HIGH stop_gained Average:44.679; most accessible tissue: Callus, score: 82.918 N N N N
vg0222556989 G -> DEL LOC_Os02g37309.1 N frameshift_variant Average:44.679; most accessible tissue: Callus, score: 82.918 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222556989 NA 2.03E-18 mr1077 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
vg0222556989 2.64E-06 NA mr1098 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
vg0222556989 4.89E-06 NA mr1101 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
vg0222556989 2.89E-06 NA mr1148 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
vg0222556989 NA 1.54E-09 mr1151 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
vg0222556989 NA 4.59E-09 mr1174 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
vg0222556989 NA 2.27E-38 mr1110_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
vg0222556989 6.81E-06 NA mr1124_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
vg0222556989 NA 5.19E-06 mr1908_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