Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0141376032:

Variant ID: vg0141376032 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41376032
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCCGACCACGGCGACGGTGGCCGACGACGGACGGACATACAGCAACATGTTCGCCGCGATGGTGGACGCCATGTACTCGGCGTTGGAGAAGGCCGGGG[C/A]
GCCGGGGGTGGCCGTCGTCGTGTCCGAGAGCGGGTGGCCGTCGGCCGGCGGCTCCGGCGCGAGCGCGGACAACGCGCGGAGGTACAACCAGGGACTGATC

Reverse complement sequence

GATCAGTCCCTGGTTGTACCTCCGCGCGTTGTCCGCGCTCGCGCCGGAGCCGCCGGCCGACGGCCACCCGCTCTCGGACACGACGACGGCCACCCCCGGC[G/T]
CCCCGGCCTTCTCCAACGCCGAGTACATGGCGTCCACCATCGCGGCGAACATGTTGCTGTATGTCCGTCCGTCGTCGGCCACCGTCGCCGTGGTCGGCTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.20% 32.30% 0.17% 0.36% NA
All Indica  2759 45.70% 53.60% 0.18% 0.51% NA
All Japonica  1512 98.40% 1.50% 0.07% 0.07% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 83.20% 16.60% 0.00% 0.17% NA
Indica II  465 12.90% 86.00% 0.00% 1.08% NA
Indica III  913 35.50% 64.40% 0.11% 0.00% NA
Indica Intermediate  786 48.70% 49.70% 0.51% 1.02% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 96.20% 3.40% 0.20% 0.20% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 71.10% 24.40% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0141376032 C -> A LOC_Os01g71410.1 missense_variant ; p.Ala276Glu; MODERATE nonsynonymous_codon ; A276E Average:71.765; most accessible tissue: Zhenshan97 young leaf, score: 78.644 benign 1.018 DELETERIOUS 0.04
vg0141376032 C -> DEL LOC_Os01g71410.1 N frameshift_variant Average:71.765; most accessible tissue: Zhenshan97 young leaf, score: 78.644 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141376032 NA 4.24E-16 Grain_length 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
vg0141376032 NA 2.10E-16 Grain_length Ind_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
vg0141376032 NA 7.49E-08 Grain_thickness Ind_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
vg0141376032 NA 5.19E-14 Grain_width Ind_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
vg0141376032 NA 4.29E-07 mr1458 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
vg0141376032 NA 6.84E-06 mr1974 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
vg0141376032 NA 7.87E-07 mr1974 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
vg0141376032 NA 1.84E-09 mr1319_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
vg0141376032 NA 5.84E-09 mr1322_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
vg0141376032 NA 1.28E-13 mr1330_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
vg0141376032 NA 1.39E-07 mr1458_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
vg0141376032 NA 2.01E-07 mr1527_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