Search for Variation information by Variation ID:

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

Detailed information for vg0815985673:

Variant ID: vg0815985673 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15985673
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGGATGACCGGATTAGTGGTTAATATACCTATTTGCGTGGTGGCGGGAATTAGACACGCTTATCTTGATCCCTGGGATCACCCCATATTGCTCCGCGTG[C/G]
CCGTGGCGCTGAAGTGTCAAAGTGCAAGTATATACAAATTACAAATCATTAGTCTAGATATATATGTATGTCTGATCTGTTGGTTTGCAGTACTCATGCA

Reverse complement sequence

TGCATGAGTACTGCAAACCAACAGATCAGACATACATATATATCTAGACTAATGATTTGTAATTTGTATATACTTGCACTTTGACACTTCAGCGCCACGG[G/C]
CACGCGGAGCAATATGGGGTGATCCCAGGGATCAAGATAAGCGTGTCTAATTCCCGCCACCACGCAAATAGGTATATTAACCACTAATCCGGTCATCCAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.10% 19.40% 0.15% 0.32% NA
All Indica  2759 98.00% 1.70% 0.07% 0.25% NA
All Japonica  1512 44.00% 55.60% 0.13% 0.26% NA
Aus  269 93.70% 4.50% 0.37% 1.49% NA
Indica I  595 98.30% 1.20% 0.34% 0.17% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 98.50% 1.10% 0.00% 0.44% NA
Indica Intermediate  786 98.00% 1.80% 0.00% 0.25% NA
Temperate Japonica  767 3.80% 96.20% 0.00% 0.00% NA
Tropical Japonica  504 95.00% 4.80% 0.00% 0.20% NA
Japonica Intermediate  241 65.60% 32.40% 0.83% 1.24% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 75.60% 22.20% 2.22% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0815985673 C -> G LOC_Os08g26230.2 missense_variant ; p.Ala134Pro; MODERATE nonsynonymous_codon ; A134P Average:63.343; most accessible tissue: Zhenshan97 root, score: 71.174 unknown unknown DELETERIOUS 0.00
vg0815985673 C -> DEL LOC_Os08g26230.2 N frameshift_variant Average:63.343; most accessible tissue: Zhenshan97 root, score: 71.174 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815985673 NA 2.10E-06 mr1013 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
vg0815985673 NA 1.63E-06 mr1031 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
vg0815985673 NA 6.86E-06 mr1087 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
vg0815985673 NA 2.92E-06 mr1330 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
vg0815985673 NA 2.93E-08 mr1449 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
vg0815985673 NA 9.63E-07 mr1584 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
vg0815985673 NA 2.58E-13 mr1844 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
vg0815985673 NA 1.33E-07 mr1844 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
vg0815985673 NA 8.76E-07 mr1870 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
vg0815985673 NA 6.49E-12 mr1879 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
vg0815985673 NA 1.21E-09 mr1087_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
vg0815985673 NA 2.89E-21 mr1308_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
vg0815985673 NA 1.81E-07 mr1308_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
vg0815985673 NA 3.73E-23 mr1361_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
vg0815985673 NA 4.72E-11 mr1361_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
vg0815985673 NA 4.24E-09 mr1584_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
vg0815985673 NA 8.38E-14 mr1853_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
vg0815985673 NA 1.42E-06 mr1853_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
vg0815985673 NA 3.64E-08 mr1952_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