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Detailed information for vg1122878285:

Variant ID: vg1122878285 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22878285
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TGATAATTTGAAGAAAAACCTCTTGGAAGTCTGCACTTATGATTATCGTGAAATCATTTTACCAGCTATGAAAGATTTCCTATGGGTTAGTCTAGTTCTT[G/A]
TATGTTATTTGACTTTGATAAATAATACTACTTTGCTTATCATTGTTTTCATGGTTGCACTCATGCAGGCTAAACTGTGTAATGTTCCACCTAAAGGGGT

Reverse complement sequence

ACCCCTTTAGGTGGAACATTACACAGTTTAGCCTGCATGAGTGCAACCATGAAAACAATGATAAGCAAAGTAGTATTATTTATCAAAGTCAAATAACATA[C/T]
AAGAACTAGACTAACCCATAGGAAATCTTTCATAGCTGGTAAAATGATTTCACGATAATCATAAGTGCAGACTTCCAAGAGGTTTTTCTTCAAATTATCA

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 78.20% 21.70% 0.08% 0.00% NA
All Indica  2759 71.80% 28.00% 0.14% 0.00% NA
All Japonica  1512 84.50% 15.50% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 31.10% 68.70% 0.17% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 82.00% 17.70% 0.22% 0.00% NA
Indica Intermediate  786 75.40% 24.40% 0.13% 0.00% NA
Temperate Japonica  767 72.90% 27.10% 0.00% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1122878285 G -> A LOC_Os11g38610.2 intron_variant ; MODIFIER silent_mutation Average:19.324; most accessible tissue: Callus, score: 26.353 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122878285 NA 8.13E-06 mr1074 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
vg1122878285 5.05E-06 NA mr1336 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
vg1122878285 6.55E-06 NA mr1336_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
vg1122878285 NA 9.44E-06 mr1923_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
vg1122878285 NA 1.27E-07 mr1933_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