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Detailed information for vg0406786851:

Variant ID: vg0406786851 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6786851
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCATCAGAGAGAGGTTGAGAATTGCACAATCTCGACAGAAGAGCTACGCAGACAACCACCGAAGGGAGCTCACTTTTGAAGCAGGGGATTATGTGTACCT[T/C]
CGTGTCACTCCGCTCCGGGGAGTGCACTGTTTCCAGACGAAAGGCAAGTTGGCACCATGTTTCGTGGGACCATACAAGATCTTGGAACGAAGAGGAGAAG

Reverse complement sequence

CTTCTCCTCTTCGTTCCAAGATCTTGTATGGTCCCACGAAACATGGTGCCAACTTGCCTTTCGTCTGGAAACAGTGCACTCCCCGGAGCGGAGTGACACG[A/G]
AGGTACACATAATCCCCTGCTTCAAAAGTGAGCTCCCTTCGGTGGTTGTCTGCGTAGCTCTTCTGTCGAGATTGTGCAATTCTCAACCTCTCTCTGATGG

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 89.20% 2.30% 7.55% 0.95% NA
All Indica  2759 85.20% 4.00% 10.87% 0.00% NA
All Japonica  1512 99.10% 0.00% 0.40% 0.46% NA
Aus  269 84.00% 0.00% 11.90% 4.09% NA
Indica I  595 91.10% 2.90% 6.05% 0.00% NA
Indica II  465 90.10% 3.90% 6.02% 0.00% NA
Indica III  913 77.80% 5.70% 16.54% 0.00% NA
Indica Intermediate  786 86.40% 2.80% 10.81% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 0.00% 0.79% 0.99% NA
Japonica Intermediate  241 98.30% 0.00% 0.83% 0.83% NA
VI/Aromatic  96 58.30% 0.00% 15.62% 26.04% NA
Intermediate  90 92.20% 1.10% 4.44% 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
vg0406786851 T -> C LOC_Os04g12290.1 synonymous_variant ; p.Leu250Leu; LOW synonymous_codon Average:37.07; most accessible tissue: Minghui63 young leaf, score: 71.254 N N N N
vg0406786851 T -> DEL LOC_Os04g12290.1 N frameshift_variant Average:37.07; most accessible tissue: Minghui63 young leaf, score: 71.254 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406786851 5.48E-06 NA mr1054 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
vg0406786851 4.47E-06 4.47E-06 mr1054 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
vg0406786851 NA 5.23E-06 mr1187 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
vg0406786851 NA 9.25E-06 mr1279 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
vg0406786851 NA 8.17E-06 mr1312 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
vg0406786851 1.90E-06 3.59E-06 mr1331 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
vg0406786851 7.64E-07 7.64E-07 mr1331 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
vg0406786851 NA 2.64E-07 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
vg0406786851 NA 1.87E-17 mr1566 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
vg0406786851 NA 3.14E-06 mr1570 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
vg0406786851 NA 5.64E-06 mr1573 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
vg0406786851 NA 2.24E-11 mr1609 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
vg0406786851 NA 6.13E-06 mr1661 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
vg0406786851 NA 9.78E-10 mr1712 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
vg0406786851 NA 2.53E-09 mr1770 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
vg0406786851 NA 2.18E-06 mr1895 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
vg0406786851 NA 6.83E-12 mr1938 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