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Detailed information for vg0320572071:

Variant ID: vg0320572071 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20572071
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.20, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGCATTCGCTACTCCGTCACCAAGAGACCAAGGATGGTGCAGGTAATTAAACTGAAATCATCCCTCAAGGGCCGTATCTATCGTTTCTGACATGTTAT[C/T]
TTAAATAATCATTCAAAGATTTCAAGATGTATTAGATGTATCACTCCGACGAACATACAAGTCAACTTCTATTAGTTATAACAAAAATGATTTGATAAAT

Reverse complement sequence

ATTTATCAAATCATTTTTGTTATAACTAATAGAAGTTGACTTGTATGTTCGTCGGAGTGATACATCTAATACATCTTGAAATCTTTGAATGATTATTTAA[G/A]
ATAACATGTCAGAAACGATAGATACGGCCCTTGAGGGATGATTTCAGTTTAATTACCTGCACCATCCTTGGTCTCTTGGTGACGGAGTAGCGAATGCAAG

Allele Frequencies:

Populations Population SizeFrequency of T(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% 0.44% NA
All Indica  2759 97.60% 2.00% 0.00% 0.33% NA
All Japonica  1512 12.70% 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 95.70% 3.70% 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 7.50% 91.30% 0.00% 1.24% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 48.90% 45.60% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0320572071 C -> T LOC_Os03g37110.1 upstream_gene_variant ; 3548.0bp to feature; MODIFIER silent_mutation Average:72.11; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N
vg0320572071 C -> T LOC_Os03g37130.1 downstream_gene_variant ; 2170.0bp to feature; MODIFIER silent_mutation Average:72.11; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N
vg0320572071 C -> T LOC_Os03g37120.1 intron_variant ; MODIFIER silent_mutation Average:72.11; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N
vg0320572071 C -> DEL N N silent_mutation Average:72.11; most accessible tissue: Zhenshan97 panicle, score: 85.665 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320572071 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
vg0320572071 NA 1.54E-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
vg0320572071 NA 8.28E-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
vg0320572071 NA 3.19E-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
vg0320572071 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
vg0320572071 NA 1.24E-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
vg0320572071 NA 2.76E-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
vg0320572071 NA 7.69E-12 mr1386 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
vg0320572071 NA 1.99E-06 mr1622 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
vg0320572071 NA 5.23E-78 mr1718 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
vg0320572071 8.66E-09 5.75E-114 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
vg0320572071 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
vg0320572071 NA 3.19E-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
vg0320572071 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
vg0320572071 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
vg0320572071 NA 6.45E-16 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
vg0320572071 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
vg0320572071 NA 6.25E-12 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
vg0320572071 2.24E-07 1.25E-114 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
vg0320572071 2.74E-10 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
vg0320572071 NA 2.05E-10 mr1893_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
vg0320572071 NA 4.71E-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
vg0320572071 8.49E-06 NA mr1987_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