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Detailed information for vg1121157956:

Variant ID: vg1121157956 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21157956
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, A: 0.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGAGTCATTGCTCACCAAACAAATTGCGGAAATTATATTTGTCCAACAACAATATTACGGGAACTCTACCAGCTCAGAGTATGGGCCAATTTACCAGC[T/A]
TAGCCAATATTGGTTTCTCTTTCAACCAGCTCACAGGGCACGTGCCTCCTGAGATTGGTAAACTAGCTAGTTTGACTCACCTTGACCTAAGTGAAAATAA

Reverse complement sequence

TTATTTTCACTTAGGTCAAGGTGAGTCAAACTAGCTAGTTTACCAATCTCAGGAGGCACGTGCCCTGTGAGCTGGTTGAAAGAGAAACCAATATTGGCTA[A/T]
GCTGGTAAATTGGCCCATACTCTGAGCTGGTAGAGTTCCCGTAATATTGTTGTTGGACAAATATAATTTCCGCAATTTGTTTGGTGAGCAATGACTCAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.70% 9.70% 1.76% 8.80% NA
All Indica  2759 84.00% 1.00% 1.41% 13.56% NA
All Japonica  1512 69.20% 27.60% 2.45% 0.73% NA
Aus  269 91.40% 0.00% 0.37% 8.18% NA
Indica I  595 96.60% 0.00% 1.01% 2.35% NA
Indica II  465 77.60% 0.60% 2.58% 19.14% NA
Indica III  913 80.00% 2.00% 0.66% 17.42% NA
Indica Intermediate  786 83.00% 0.90% 1.91% 14.25% NA
Temperate Japonica  767 90.60% 6.00% 2.48% 0.91% NA
Tropical Japonica  504 36.30% 60.70% 2.58% 0.40% NA
Japonica Intermediate  241 69.70% 27.40% 2.07% 0.83% NA
VI/Aromatic  96 93.80% 3.10% 0.00% 3.12% NA
Intermediate  90 75.60% 11.10% 6.67% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1121157956 T -> A LOC_Os11g36000.1 missense_variant ; p.Leu334Ile; MODERATE nonsynonymous_codon ; L334I Average:49.108; most accessible tissue: Callus, score: 84.645 unknown unknown TOLERATED 0.05
vg1121157956 T -> DEL LOC_Os11g36000.1 N frameshift_variant Average:49.108; most accessible tissue: Callus, score: 84.645 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121157956 NA 4.17E-06 mr1502 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
vg1121157956 NA 9.43E-06 mr1502 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
vg1121157956 NA 5.24E-06 mr1543 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
vg1121157956 NA 5.78E-09 mr1648 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
vg1121157956 NA 7.96E-13 mr1871 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
vg1121157956 NA 6.19E-12 mr1398_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
vg1121157956 NA 1.86E-08 mr1398_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
vg1121157956 NA 3.34E-07 mr1551_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
vg1121157956 NA 2.55E-07 mr1696_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
vg1121157956 NA 2.30E-09 mr1705_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
vg1121157956 NA 9.33E-13 mr1993_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