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

Detailed information for vg0320151239:

Variant ID: vg0320151239 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20151239
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGAGCTGGAGAAGAGATGCGGATGGGCGGCCTTCAACTCATCTTCCCTTTCCCAGGTTGCCTTTTCCTCTGAATGGTGGCTCCACTGAACCCTGGAGAG[T/C]
CTAGTGACCTTGTTTCTGGTTCTTCTTTCACTGGTCTCAAGGATGCGAACTGGCTTCTCCACGTAGGTCAGATCCTCTTGGATATCGATGTGCTCCGAAT

Reverse complement sequence

ATTCGGAGCACATCGATATCCAAGAGGATCTGACCTACGTGGAGAAGCCAGTTCGCATCCTTGAGACCAGTGAAAGAAGAACCAGAAACAAGGTCACTAG[A/G]
CTCTCCAGGGTTCAGTGGAGCCACCATTCAGAGGAAAAGGCAACCTGGGAAAGGGAAGATGAGTTGAAGGCCGCCCATCCGCATCTCTTCTCCAGCTCCT

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 57.80% 37.50% 2.31% 2.35% NA
All Indica  2759 84.10% 11.50% 2.57% 1.92% NA
All Japonica  1512 11.70% 86.70% 0.20% 1.39% NA
Aus  269 65.10% 10.00% 11.90% 13.01% NA
Indica I  595 57.50% 33.30% 6.72% 2.52% NA
Indica II  465 93.10% 5.60% 0.43% 0.86% NA
Indica III  913 96.10% 1.30% 0.33% 2.30% NA
Indica Intermediate  786 84.90% 10.20% 3.31% 1.65% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 31.20% 68.30% 0.20% 0.40% NA
Japonica Intermediate  241 7.50% 83.80% 0.83% 7.88% NA
VI/Aromatic  96 25.00% 75.00% 0.00% 0.00% NA
Intermediate  90 42.20% 52.20% 3.33% 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
vg0320151239 T -> C LOC_Os03g36330.1 synonymous_variant ; p.Arg719Arg; LOW synonymous_codon Average:25.377; most accessible tissue: Minghui63 young leaf, score: 50.756 N N N N
vg0320151239 T -> DEL LOC_Os03g36330.1 N frameshift_variant Average:25.377; most accessible tissue: Minghui63 young leaf, score: 50.756 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0320151239 NA 1.73E-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
vg0320151239 NA 4.49E-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
vg0320151239 NA 4.62E-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
vg0320151239 NA 9.82E-09 mr1718 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
vg0320151239 7.14E-06 NA 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
vg0320151239 3.62E-09 3.45E-18 mr1750 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
vg0320151239 NA 6.70E-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
vg0320151239 1.79E-06 1.79E-06 mr1987 Ind_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
vg0320151239 NA 2.78E-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
vg0320151239 NA 5.04E-07 mr1188_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
vg0320151239 NA 9.56E-13 mr1217_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
vg0320151239 NA 5.99E-15 mr1718_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
vg0320151239 NA 3.67E-11 mr1722_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
vg0320151239 3.56E-06 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
vg0320151239 8.36E-11 1.76E-23 mr1750_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
vg0320151239 NA 1.35E-07 mr1987_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