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Detailed information for vg1125863777:

Variant ID: vg1125863777 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25863777
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.58, G: 0.43, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTACTGTTGCTTCTAATAACACCTATATATATTGGCTGCATTTTTCCTTTCATGTAGACACTGTTTGTGGATGTTTGGTGAAGTTGATAGTGTATCT[G/A]
ACAGAGGGGGAATCTTTGCAGAATTAGTTCATGATGTGATAGAGCGAAAGTGTATCTTGAAATGGAACACTATCACTACAATTCAATCAAAATATGCACT

Reverse complement sequence

AGTGCATATTTTGATTGAATTGTAGTGATAGTGTTCCATTTCAAGATACACTTTCGCTCTATCACATCATGAACTAATTCTGCAAAGATTCCCCCTCTGT[C/T]
AGATACACTATCAACTTCACCAAACATCCACAAACAGTGTCTACATGAAAGGAAAAATGCAGCCAATATATATAGGTGTTATTAGAAGCAACAGTAAAAT

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 35.80% 27.00% 12.76% 24.42% NA
All Indica  2759 52.40% 17.60% 12.58% 17.43% NA
All Japonica  1512 8.90% 42.80% 12.10% 36.24% NA
Aus  269 26.00% 25.70% 23.05% 25.28% NA
Indica I  595 53.30% 43.00% 1.68% 2.02% NA
Indica II  465 36.30% 5.80% 36.77% 21.08% NA
Indica III  913 55.40% 11.40% 8.11% 25.08% NA
Indica Intermediate  786 57.60% 12.60% 11.70% 18.07% NA
Temperate Japonica  767 7.80% 62.20% 6.13% 23.86% NA
Tropical Japonica  504 10.30% 13.50% 19.25% 56.94% NA
Japonica Intermediate  241 9.10% 42.30% 16.18% 32.37% NA
VI/Aromatic  96 3.10% 54.20% 5.21% 37.50% NA
Intermediate  90 43.30% 26.70% 6.67% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125863777 G -> A LOC_Os11g42910.1 missense_variant ; p.Asp973Asn; MODERATE nonsynonymous_codon ; D973N Average:30.827; most accessible tissue: Zhenshan97 young leaf, score: 51.997 benign -1.181 TOLERATED 0.33
vg1125863777 G -> DEL LOC_Os11g42910.1 N frameshift_variant Average:30.827; most accessible tissue: Zhenshan97 young leaf, score: 51.997 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125863777 3.67E-06 NA Plant_height Jap_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1125863777 5.67E-12 1.98E-20 mr1191 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
vg1125863777 2.33E-07 8.92E-11 mr1191 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
vg1125863777 3.89E-15 2.64E-27 mr1644 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
vg1125863777 1.07E-08 7.41E-15 mr1644 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
vg1125863777 6.27E-08 6.27E-08 mr1644 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
vg1125863777 3.95E-14 2.92E-31 mr1191_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
vg1125863777 2.14E-08 6.09E-16 mr1191_2 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
vg1125863777 1.02E-07 1.02E-07 mr1191_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
vg1125863777 NA 3.71E-06 mr1380_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
vg1125863777 NA 3.63E-06 mr1462_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
vg1125863777 NA 1.70E-06 mr1561_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
vg1125863777 NA 2.61E-07 mr1875_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
vg1125863777 NA 6.36E-06 mr1908_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