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Detailed information for vg0619886632:

Variant ID: vg0619886632 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19886632
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


AGATGGCACAATTATTCCTCAAGTTATTCCTGAACATTTGGTGCGTAATATTCAGCCAGACCTTCAAAATTACCAAGGGGGCAATTTGAATTATCAATAT[C/T]
AGCCACCATCGCCTCATGTTCAGTACCAGCAGGCAGGATCGGCTCAACCCCAATTTGTCCCTCACTACAATCAATTTGAGCCTATGCCACAACAACCTCA

Reverse complement sequence

TGAGGTTGTTGTGGCATAGGCTCAAATTGATTGTAGTGAGGGACAAATTGGGGTTGAGCCGATCCTGCCTGCTGGTACTGAACATGAGGCGATGGTGGCT[G/A]
ATATTGATAATTCAAATTGCCCCCTTGGTAATTTTGAAGGTCTGGCTGAATATTACGCACCAAATGTTCAGGAATAACTTGAGGAATAATTGTGCCATCT

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 36.40% 0.40% 1.52% 61.74% NA
All Indica  2759 7.80% 0.40% 1.20% 90.65% NA
All Japonica  1512 96.00% 0.10% 0.26% 3.70% NA
Aus  269 1.90% 1.10% 0.37% 96.65% NA
Indica I  595 2.50% 0.20% 1.68% 95.63% NA
Indica II  465 7.70% 0.60% 0.65% 90.97% NA
Indica III  913 10.60% 0.40% 1.20% 87.73% NA
Indica Intermediate  786 8.50% 0.30% 1.15% 90.08% NA
Temperate Japonica  767 97.10% 0.10% 0.13% 2.61% NA
Tropical Japonica  504 93.70% 0.00% 0.20% 6.15% NA
Japonica Intermediate  241 97.10% 0.00% 0.83% 2.07% NA
VI/Aromatic  96 3.10% 2.10% 29.17% 65.62% NA
Intermediate  90 50.00% 1.10% 6.67% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0619886632 C -> T LOC_Os06g34140.1 intron_variant ; MODIFIER silent_mutation Average:13.666; most accessible tissue: Callus, score: 21.393 N N N N
vg0619886632 C -> DEL N N silent_mutation Average:13.666; most accessible tissue: Callus, score: 21.393 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619886632 NA 3.47E-07 mr1408_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
vg0619886632 NA 7.64E-06 mr1482_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
vg0619886632 NA 2.11E-06 mr1691_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
vg0619886632 NA 1.05E-06 mr1727_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
vg0619886632 8.24E-06 NA mr1743_2 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
vg0619886632 6.74E-07 1.01E-06 mr1743_2 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
vg0619886632 NA 1.04E-06 mr1866_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
vg0619886632 NA 2.65E-06 mr1915_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
vg0619886632 NA 6.14E-09 mr1947_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
vg0619886632 8.02E-06 8.02E-06 mr1947_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
vg0619886632 6.81E-06 1.48E-06 mr1986_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