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Detailed information for vg0219878821:

Variant ID: vg0219878821 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19878821
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


CATCCTTGGCGGCAAGTGAGAGGCCGCGGCGACGCTCGCTAGCTAATGACCTGCCACTTGGCCCCTTTTTTTCTTGTTCCTCACAACCTTGGCACGGCCA[T/C]
AGGCAGATCTCACGGTGACAAAAATCGGCACTAGAGGTCGCGGCGGTGGAAATCGACCCTAGAGGCCGAGGCGATGCTCCCTGCGGCGGCACTGGAGGTC

Reverse complement sequence

GACCTCCAGTGCCGCCGCAGGGAGCATCGCCTCGGCCTCTAGGGTCGATTTCCACCGCCGCGACCTCTAGTGCCGATTTTTGTCACCGTGAGATCTGCCT[A/G]
TGGCCGTGCCAAGGTTGTGAGGAACAAGAAAAAAAGGGGCCAAGTGGCAGGTCATTAGCTAGCGAGCGTCGCCGCGGCCTCTCACTTGCCGCCAAGGATG

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 24.60% 24.50% 1.82% 49.09% NA
All Indica  2759 7.10% 8.40% 2.65% 81.81% NA
All Japonica  1512 45.50% 52.60% 0.20% 1.65% NA
Aus  269 58.00% 34.20% 2.97% 4.83% NA
Indica I  595 9.40% 7.70% 1.01% 81.85% NA
Indica II  465 3.20% 15.10% 2.15% 79.57% NA
Indica III  913 5.10% 4.50% 4.38% 85.98% NA
Indica Intermediate  786 9.90% 9.70% 2.16% 78.24% NA
Temperate Japonica  767 56.30% 42.40% 0.26% 1.04% NA
Tropical Japonica  504 20.80% 77.60% 0.00% 1.59% NA
Japonica Intermediate  241 62.70% 33.20% 0.41% 3.73% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 32.20% 37.80% 2.22% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0219878821 T -> DEL N N silent_mutation Average:58.507; most accessible tissue: Zhenshan97 young leaf, score: 80.848 N N N N
vg0219878821 T -> C LOC_Os02g33440.1 upstream_gene_variant ; 98.0bp to feature; MODIFIER silent_mutation Average:58.507; most accessible tissue: Zhenshan97 young leaf, score: 80.848 N N N N
vg0219878821 T -> C LOC_Os02g33450.1 upstream_gene_variant ; 3231.0bp to feature; MODIFIER silent_mutation Average:58.507; most accessible tissue: Zhenshan97 young leaf, score: 80.848 N N N N
vg0219878821 T -> C LOC_Os02g33450.2 upstream_gene_variant ; 3231.0bp to feature; MODIFIER silent_mutation Average:58.507; most accessible tissue: Zhenshan97 young leaf, score: 80.848 N N N N
vg0219878821 T -> C LOC_Os02g33440-LOC_Os02g33450 intergenic_region ; MODIFIER silent_mutation Average:58.507; most accessible tissue: Zhenshan97 young leaf, score: 80.848 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219878821 NA 8.91E-09 mr1082 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
vg0219878821 NA 3.32E-07 mr1083 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
vg0219878821 NA 1.44E-06 mr1085 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
vg0219878821 NA 2.93E-11 mr1093 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
vg0219878821 NA 3.83E-07 mr1103 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
vg0219878821 NA 2.96E-06 mr1107 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
vg0219878821 NA 5.20E-08 mr1226 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
vg0219878821 NA 1.42E-09 mr1301 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
vg0219878821 NA 9.64E-10 mr1354 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
vg0219878821 NA 4.09E-13 mr1379 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
vg0219878821 NA 2.00E-06 mr1387 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
vg0219878821 NA 9.76E-07 mr1408 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
vg0219878821 NA 1.22E-07 mr1410 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
vg0219878821 NA 2.60E-07 mr1411 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
vg0219878821 NA 2.25E-06 mr1518 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
vg0219878821 NA 1.07E-10 mr1559 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
vg0219878821 NA 1.49E-07 mr1560 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
vg0219878821 NA 7.42E-06 mr1590 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
vg0219878821 NA 1.32E-08 mr1637 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
vg0219878821 NA 9.08E-06 mr1676 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
vg0219878821 NA 1.96E-06 mr1807 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
vg0219878821 1.22E-06 1.22E-06 mr1866 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
vg0219878821 NA 6.11E-07 mr1964 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
vg0219878821 NA 2.61E-09 mr1379_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
vg0219878821 NA 5.98E-10 mr1559_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
vg0219878821 NA 1.50E-06 mr1559_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