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Detailed information for vg1117964950:

Variant ID: vg1117964950 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17964950
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTTTGAACGGCCATAACTCCGGCCAGGGTGGTTAGGTCGGGTGCTTGAGTTTCTTCATTGCTAGTTGACGCCCAACGTCGGCTTGCCATCTGTGTAGAT[C/T]
GATTAGATAAGTAACTCAATTTCCTAACTAGCCCTTATGGTTTTATCCCGTTAAGGGAGTTGTTTTGATGTGAACTTTGTTTTGCAAGCATGGTGGAATA

Reverse complement sequence

TATTCCACCATGCTTGCAAAACAAAGTTCACATCAAAACAACTCCCTTAACGGGATAAAACCATAAGGGCTAGTTAGGAAATTGAGTTACTTATCTAATC[G/A]
ATCTACACAGATGGCAAGCCGACGTTGGGCGTCAACTAGCAATGAAGAAACTCAAGCACCCGACCTAACCACCCTGGCCGGAGTTATGGCCGTTCAAACC

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 71.20% 7.90% 2.05% 18.94% NA
All Indica  2759 73.40% 4.20% 2.65% 19.79% NA
All Japonica  1512 76.10% 3.90% 0.40% 19.64% NA
Aus  269 26.40% 69.50% 2.60% 1.49% NA
Indica I  595 72.30% 5.40% 1.51% 20.84% NA
Indica II  465 88.80% 0.60% 1.51% 9.03% NA
Indica III  913 65.10% 5.50% 4.16% 25.30% NA
Indica Intermediate  786 74.80% 3.80% 2.42% 18.96% NA
Temperate Japonica  767 95.70% 2.20% 0.26% 1.83% NA
Tropical Japonica  504 59.70% 1.80% 0.60% 37.90% NA
Japonica Intermediate  241 47.70% 13.70% 0.41% 38.17% NA
VI/Aromatic  96 44.80% 6.20% 11.46% 37.50% NA
Intermediate  90 82.20% 4.40% 0.00% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117964950 C -> T LOC_Os11g30850.1 upstream_gene_variant ; 3200.0bp to feature; MODIFIER silent_mutation Average:54.848; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N
vg1117964950 C -> T LOC_Os11g30860.1 upstream_gene_variant ; 11.0bp to feature; MODIFIER silent_mutation Average:54.848; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N
vg1117964950 C -> T LOC_Os11g30860-LOC_Os11g30880 intergenic_region ; MODIFIER silent_mutation Average:54.848; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N
vg1117964950 C -> DEL N N silent_mutation Average:54.848; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117964950 NA 3.49E-06 mr1073 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
vg1117964950 NA 2.41E-17 mr1113 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
vg1117964950 NA 2.49E-21 mr1114 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
vg1117964950 NA 5.30E-20 mr1117 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
vg1117964950 NA 2.45E-17 mr1119 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
vg1117964950 NA 1.20E-22 mr1120 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
vg1117964950 NA 4.49E-08 mr1262 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
vg1117964950 NA 1.70E-06 mr1382 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
vg1117964950 NA 1.13E-13 mr1409 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
vg1117964950 1.09E-06 8.30E-10 mr1417 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
vg1117964950 NA 5.18E-14 mr1496 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
vg1117964950 NA 8.08E-37 mr1549 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
vg1117964950 NA 1.89E-46 mr1550 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
vg1117964950 NA 7.44E-07 mr1931 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
vg1117964950 NA 5.96E-21 mr1961 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
vg1117964950 NA 2.80E-16 mr1260_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
vg1117964950 NA 7.43E-47 mr1550_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