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Detailed information for vg0810860589:

Variant ID: vg0810860589 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10860589
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTTGAACCATTAAAACACCTTGTCAATGTATGTACTCTGGCTTAATCCAATTAGCCTCTTTGATGTATCTCTATAGATCCTTATGCCCAGAATATATG[C/T]
TGTTTCCCCTAAGTCCTTCATTGAAAAACTATTTTTCAACGATGTCTTAACGGATTCAAGCATAGGAATATCGTTCCCAATCAATAATATGTCATCTACA

Reverse complement sequence

TGTAGATGACATATTATTGATTGGGAACGATATTCCTATGCTTGAATCCGTTAAGACATCGTTGAAAAATAGTTTTTCAATGAAGGACTTAGGGGAAACA[G/A]
CATATATTCTGGGCATAAGGATCTATAGAGATACATCAAAGAGGCTAATTGGATTAAGCCAGAGTACATACATTGACAAGGTGTTTTAATGGTTCAACAT

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 88.00% 1.00% 3.91% 7.11% NA
All Indica  2759 99.90% 0.00% 0.07% 0.04% NA
All Japonica  1512 67.30% 3.10% 10.52% 19.11% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.00% 0.22% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 91.40% 4.30% 2.74% 1.56% NA
Tropical Japonica  504 41.90% 0.20% 17.66% 40.28% NA
Japonica Intermediate  241 43.60% 5.40% 20.33% 30.71% NA
VI/Aromatic  96 39.60% 0.00% 20.83% 39.58% NA
Intermediate  90 85.60% 1.10% 4.44% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0810860589 C -> T LOC_Os08g17750.1 missense_variant ; p.Ala1135Thr; MODERATE nonsynonymous_codon ; A1135T Average:26.722; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 benign 0.117 TOLERATED 0.17
vg0810860589 C -> DEL LOC_Os08g17750.1 N frameshift_variant Average:26.722; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810860589 NA 7.11E-17 Grain_length Jap_All Not 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
vg0810860589 NA 2.15E-12 Grain_weight All Not 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
vg0810860589 NA 2.80E-08 Grain_weight 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
vg0810860589 NA 8.52E-12 mr1084 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
vg0810860589 NA 3.41E-06 mr1179 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
vg0810860589 NA 2.72E-13 mr1205 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
vg0810860589 NA 7.65E-06 mr1205 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
vg0810860589 NA 7.79E-06 mr1215 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
vg0810860589 NA 1.75E-06 mr1229 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
vg0810860589 NA 3.44E-07 mr1236 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
vg0810860589 NA 4.47E-13 mr1330 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
vg0810860589 NA 4.02E-09 mr1332 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
vg0810860589 NA 4.77E-06 mr1374 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
vg0810860589 4.50E-06 4.49E-06 mr1597 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
vg0810860589 2.67E-06 2.67E-06 mr1597 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
vg0810860589 NA 5.92E-06 mr1763 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
vg0810860589 NA 5.18E-09 mr1379_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
vg0810860589 NA 1.21E-06 mr1559_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
vg0810860589 NA 1.79E-08 mr1905_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