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Detailed information for vg0816932118:

Variant ID: vg0816932118 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16932118
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.30, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


CGCTTGCGCGGGTAGCTTTGTGTGTTTACTGTGGAATTGACAGGTTTCACATCGCTGGACCATGTCGCATGCATCTTTAAGGGCGGTTGGCCAGAAAAAG[T/C]
CTTGTCGAAAAGCTTTGCTGACCAATGTCCGACCGGCGGCGTGTGACCCACATATGCCTTCATGTATGTCGAGGAGGAGGTGTCTGCCGTCGTCGGTAGA

Reverse complement sequence

TCTACCGACGACGGCAGACACCTCCTCCTCGACATACATGAAGGCATATGTGGGTCACACGCCGCCGGTCGGACATTGGTCAGCAAAGCTTTTCGACAAG[A/G]
CTTTTTCTGGCCAACCGCCCTTAAAGATGCATGCGACATGGTCCAGCGATGTGAAACCTGTCAATTCCACAGTAAACACACAAAGCTACCCGCGCAAGCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 31.00% 17.20% 1.44% 50.42% NA
All Indica  2759 17.30% 23.20% 1.85% 57.59% NA
All Japonica  1512 52.60% 6.50% 0.86% 39.95% NA
Aus  269 58.00% 21.20% 0.00% 20.82% NA
Indica I  595 33.80% 39.00% 0.50% 26.72% NA
Indica II  465 7.30% 8.40% 1.94% 82.37% NA
Indica III  913 12.50% 21.60% 2.96% 62.98% NA
Indica Intermediate  786 16.40% 22.00% 1.53% 60.05% NA
Temperate Japonica  767 72.80% 2.00% 0.78% 24.51% NA
Tropical Japonica  504 24.00% 15.90% 0.99% 59.13% NA
Japonica Intermediate  241 48.50% 1.70% 0.83% 48.96% NA
VI/Aromatic  96 7.30% 1.00% 1.04% 90.62% NA
Intermediate  90 28.90% 15.60% 3.33% 52.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0816932118 T -> C LOC_Os08g27800.1 missense_variant ; p.Asp1233Gly; MODERATE nonsynonymous_codon ; D1233G Average:21.855; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 unknown unknown TOLERATED 1.00
vg0816932118 T -> DEL LOC_Os08g27800.1 N frameshift_variant Average:21.855; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816932118 NA 1.73E-06 mr1401 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
vg0816932118 NA 8.87E-10 mr1089_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
vg0816932118 NA 1.37E-10 mr1093_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
vg0816932118 NA 7.69E-06 mr1109_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
vg0816932118 NA 3.13E-07 mr1129_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
vg0816932118 NA 5.30E-07 mr1248_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
vg0816932118 NA 2.00E-08 mr1251_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
vg0816932118 NA 3.73E-07 mr1257_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
vg0816932118 NA 7.94E-10 mr1423_2 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
vg0816932118 NA 2.18E-08 mr1435_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
vg0816932118 NA 1.16E-08 mr1599_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