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Detailed information for vg1100991046:

Variant ID: vg1100991046 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 991046
Reference Allele: GAlternative Allele: A,T
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.16, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


AGGTGAGGTACATGAGGGAATTTGTGTTACTCATCAATCGGCTCACAAGATGAAGTGGTTACTTTGGCGTGCAGGGTATTTTTGGCCGACAATGTTGGAA[G/A,T]
ATTGTTTCAGATATTATAGAGGATGTCAAGATTGTCAAAAATTTGGAGCAATTCAAAGAGCACCAGCATCGGCTATGAATCCTATTATCAAGCCGTGGCC

Reverse complement sequence

GGCCACGGCTTGATAATAGGATTCATAGCCGATGCTGGTGCTCTTTGAATTGCTCCAAATTTTTGACAATCTTGACATCCTCTATAATATCTGAAACAAT[C/T,A]
TTCCAACATTGTCGGCCAAAAATACCCTGCACGCCAAAGTAACCACTTCATCTTGTGAGCCGATTGATGAGTAACACAAATTCCCTCATGTACCTCACCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.30% 35.90% 0.42% 3.41% NA
All Indica  2759 92.90% 4.50% 0.36% 2.28% NA
All Japonica  1512 2.00% 97.70% 0.00% 0.33% NA
Aus  269 56.10% 8.60% 3.72% 31.60% NA
Indica I  595 97.30% 2.00% 0.50% 0.17% NA
Indica II  465 84.10% 13.30% 0.65% 1.94% NA
Indica III  913 96.90% 0.30% 0.22% 2.52% NA
Indica Intermediate  786 90.10% 5.90% 0.25% 3.82% NA
Temperate Japonica  767 2.50% 97.50% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 98.60% 0.00% 0.40% NA
Japonica Intermediate  241 2.50% 96.30% 0.00% 1.24% NA
VI/Aromatic  96 69.80% 25.00% 0.00% 5.21% NA
Intermediate  90 41.10% 55.60% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1100991046 G -> T LOC_Os11g02890.1 missense_variant ; p.Lys1034Asn; MODERATE N Average:31.671; most accessible tissue: Zhenshan97 young leaf, score: 43.913 N N N N
vg1100991046 G -> A LOC_Os11g02890.1 synonymous_variant ; p.Lys1034Lys; LOW nonsynonymous_codon ; K1034I Average:31.671; most accessible tissue: Zhenshan97 young leaf, score: 43.913 unknown unknown DELETERIOUS 0.02
vg1100991046 G -> DEL LOC_Os11g02890.1 N frameshift_variant Average:31.671; most accessible tissue: Zhenshan97 young leaf, score: 43.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100991046 NA 3.93E-07 mr1093 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
vg1100991046 NA 6.57E-29 mr1226 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
vg1100991046 NA 2.84E-06 mr1235 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
vg1100991046 4.65E-06 1.13E-37 mr1243 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
vg1100991046 NA 5.28E-07 mr1243 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
vg1100991046 NA 1.84E-26 mr1251 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
vg1100991046 NA 4.67E-31 mr1257 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
vg1100991046 NA 5.63E-06 mr1257 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
vg1100991046 NA 1.47E-06 mr1408 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
vg1100991046 NA 4.03E-27 mr1411 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
vg1100991046 NA 4.42E-36 mr1435 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
vg1100991046 NA 2.71E-22 mr1888 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
vg1100991046 NA 2.42E-13 mr1982 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
vg1100991046 NA 2.91E-07 mr1548_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