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Detailed information for vg0317664128:

Variant ID: vg0317664128 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17664128
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGTATGTACATCTTTGACAATATTATAAAAAATAGTATAATTTAAAATGACACCAATCTGAACAGCCCGTTAGTTCTTTTTGGGTTTGTTTTTGGGTGT[G/C]
TGCAGCAGACTGTCTATGAATGCATTTCGTCCTTTTGGTCTGAAAAACAATAGCTGCACAGATATAAGTTAAGCTTGCTTCCGGAAGTTAGTGACTTATA

Reverse complement sequence

TATAAGTCACTAACTTCCGGAAGCAAGCTTAACTTATATCTGTGCAGCTATTGTTTTTCAGACCAAAAGGACGAAATGCATTCATAGACAGTCTGCTGCA[C/G]
ACACCCAAAAACAAACCCAAAAAGAACTAACGGGCTGTTCAGATTGGTGTCATTTTAAATTATACTATTTTTTATAATATTGTCAAAGATGTACATACAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.00% 42.00% 0.00% 0.00% NA
All Indica  2759 87.40% 12.60% 0.00% 0.00% NA
All Japonica  1512 0.70% 99.30% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 64.70% 35.30% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 94.50% 5.50% 0.00% 0.00% NA
Indica Intermediate  786 90.50% 9.50% 0.00% 0.00% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 45.60% 54.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0317664128 G -> C LOC_Os03g31000.1 intron_variant ; MODIFIER silent_mutation Average:39.53; most accessible tissue: Zhenshan97 panicle, score: 73.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317664128 NA 2.44E-11 mr1070 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
vg0317664128 NA 7.04E-09 mr1198 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
vg0317664128 NA 1.09E-07 mr1274 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
vg0317664128 NA 3.18E-13 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
vg0317664128 NA 3.15E-07 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
vg0317664128 1.16E-09 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
vg0317664128 7.56E-09 1.15E-13 mr1750_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