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Detailed information for vg0320571981:

Variant ID: vg0320571981 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20571981
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGACGGACGACTTCAGGGAGCTCGCTGACCCCGCGCTGGAGCGCCGCTACTCCAAGTCGGAGATGCGGAGGATGGTGGAGGCCGCGGCCGCTTGCATTCG[C/G]
TACTCCGTCACCAAGAGACCAAGGATGGTGCAGGTAATTAAACTGAAATCATCCCTCAAGGGCCGTATCTATCGTTTCTGACATGTTATCTTAAATAATC

Reverse complement sequence

GATTATTTAAGATAACATGTCAGAAACGATAGATACGGCCCTTGAGGGATGATTTCAGTTTAATTACCTGCACCATCCTTGGTCTCTTGGTGACGGAGTA[G/C]
CGAATGCAAGCGGCCGCGGCCTCCACCATCCTCCGCATCTCCGACTTGGAGTAGCGGCGCTCCAGCGCGGGGTCAGCGAGCTCCCTGAAGTCGTCCGTCT

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 67.50% 32.00% 0.00% 0.42% NA
All Indica  2759 97.60% 2.10% 0.00% 0.33% NA
All Japonica  1512 12.80% 86.80% 0.00% 0.46% NA
Aus  269 88.50% 11.50% 0.00% 0.00% NA
Indica I  595 98.70% 1.00% 0.00% 0.34% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 98.80% 1.00% 0.00% 0.22% NA
Indica Intermediate  786 95.50% 3.80% 0.00% 0.64% NA
Temperate Japonica  767 0.30% 99.60% 0.00% 0.13% NA
Tropical Japonica  504 34.10% 65.30% 0.00% 0.60% NA
Japonica Intermediate  241 7.90% 90.90% 0.00% 1.24% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 50.00% 45.60% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0320571981 C -> DEL LOC_Os03g37120.1 N frameshift_variant Average:74.964; most accessible tissue: Zhenshan97 panicle, score: 86.058 N N N N
vg0320571981 C -> G LOC_Os03g37120.1 synonymous_variant ; p.Arg599Arg; LOW synonymous_codon Average:74.964; most accessible tissue: Zhenshan97 panicle, score: 86.058 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320571981 NA 3.38E-07 mr1136 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
vg0320571981 NA 6.00E-11 mr1188 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
vg0320571981 NA 7.80E-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
vg0320571981 NA 2.49E-21 mr1217 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
vg0320571981 NA 1.48E-07 mr1217 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
vg0320571981 NA 1.42E-07 mr1227 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
vg0320571981 NA 8.73E-18 mr1304 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
vg0320571981 8.96E-10 7.64E-116 mr1750 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
vg0320571981 NA 2.41E-06 mr1830 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
vg0320571981 NA 2.07E-19 mr1845 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
vg0320571981 NA 4.09E-07 mr1845 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
vg0320571981 NA 7.10E-08 mr1852 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
vg0320571981 NA 8.22E-15 mr1933 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
vg0320571981 NA 1.76E-08 mr1136_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
vg0320571981 NA 1.32E-11 mr1188_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
vg0320571981 NA 1.24E-107 mr1718_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
vg0320571981 1.12E-11 NA mr1750_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
vg0320571981 NA 1.30E-13 mr1827_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
vg0320571981 NA 3.48E-22 mr1933_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