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Detailed information for vg0416678941:

Variant ID: vg0416678941 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 16678941
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TGTACTACCAAACAGTATCGTCGACCCCATCAACGATATTTGACCCGCTGTTGCCCGGAATCTTTTCTTCAGTTCTGGACTAACTCCATATATCTCAACT[C/T]
CTCATCAAGTCCCAGATATATCATGTTTCCACCGAATAATTCCATATGCAACCTGACTAGCCTGTTGCCGCCAGTCTACTCGCCCTTTGCACTTGCAAAC

Reverse complement sequence

GTTTGCAAGTGCAAAGGGCGAGTAGACTGGCGGCAACAGGCTAGTCAGGTTGCATATGGAATTATTCGGTGGAAACATGATATATCTGGGACTTGATGAG[G/A]
AGTTGAGATATATGGAGTTAGTCCAGAACTGAAGAAAAGATTCCGGGCAACAGCGGGTCAAATATCGTTGATGGGGTCGACGATACTGTTTGGTAGTACA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.80% 12.00% 15.02% 0.17% NA
All Indica  2759 58.90% 19.70% 21.20% 0.22% NA
All Japonica  1512 91.70% 1.10% 7.14% 0.07% NA
Aus  269 97.80% 0.70% 1.49% 0.00% NA
Indica I  595 65.40% 15.50% 19.16% 0.00% NA
Indica II  465 43.70% 31.20% 25.16% 0.00% NA
Indica III  913 63.60% 17.00% 18.84% 0.55% NA
Indica Intermediate  786 57.50% 19.20% 23.16% 0.13% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 76.40% 3.00% 20.44% 0.20% NA
Japonica Intermediate  241 97.10% 0.80% 2.07% 0.00% NA
VI/Aromatic  96 96.90% 1.00% 2.08% 0.00% NA
Intermediate  90 80.00% 6.70% 12.22% 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
vg0416678941 C -> DEL N N silent_mutation Average:36.041; most accessible tissue: Minghui63 flag leaf, score: 62.47 N N N N
vg0416678941 C -> T LOC_Os04g28220.1 intron_variant ; MODIFIER silent_mutation Average:36.041; most accessible tissue: Minghui63 flag leaf, score: 62.47 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0416678941 2.01E-06 2.01E-06 mr1370 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
vg0416678941 5.66E-06 9.77E-06 mr1398 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
vg0416678941 2.09E-06 2.09E-06 mr1463 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
vg0416678941 NA 1.79E-07 mr1584 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
vg0416678941 NA 2.71E-06 mr1866 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
vg0416678941 NA 4.69E-06 mr1498_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