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Detailed information for vg0910353994:

Variant ID: vg0910353994 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10353994
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGACACATTTAAAGAATGTGGAGTATGGTAGAGATTTTGTGAATAAATCAGCAAGATTATCACATGACTTAGTTTGTAAGATGTTTATCTCTCCATGTTG[C/T]
TGAAACTCATGAGGATAAAATAATTTAGGAGCAATATGCTTAGTGATGTTACTCTTAATATAACCAATTTCCATCTGAACAACACAAGCGGCATTATCTT

Reverse complement sequence

AAGATAATGCCGCTTGTGTTGTTCAGATGGAAATTGGTTATATTAAGAGTAACATCACTAAGCATATTGCTCCTAAATTATTTTATCCTCATGAGTTTCA[G/A]
CAACATGGAGAGATAAACATCTTACAAACTAAGTCATGTGATAATCTTGCTGATTTATTCACAAAATCTCTACCATACTCCACATTCTTTAAATGTGTCA

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 22.40% 0.10% 35.67% 41.77% NA
All Indica  2759 14.50% 0.00% 23.92% 61.58% NA
All Japonica  1512 38.50% 0.30% 48.61% 12.57% NA
Aus  269 4.80% 0.40% 75.46% 19.33% NA
Indica I  595 9.60% 0.00% 6.05% 84.37% NA
Indica II  465 36.10% 0.00% 21.51% 42.37% NA
Indica III  913 4.50% 0.00% 38.34% 57.17% NA
Indica Intermediate  786 16.90% 0.10% 22.14% 60.81% NA
Temperate Japonica  767 63.00% 0.30% 21.90% 14.86% NA
Tropical Japonica  504 7.30% 0.40% 83.13% 9.13% NA
Japonica Intermediate  241 25.70% 0.40% 61.41% 12.45% NA
VI/Aromatic  96 26.00% 0.00% 61.46% 12.50% NA
Intermediate  90 44.40% 0.00% 32.22% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0910353994 C -> DEL LOC_Os09g16930.1 N frameshift_variant Average:11.894; most accessible tissue: Callus, score: 22.81 N N N N
vg0910353994 C -> T LOC_Os09g16930.1 synonymous_variant ; p.Gln1037Gln; LOW synonymous_codon Average:11.894; most accessible tissue: Callus, score: 22.81 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0910353994 NA 6.61E-09 mr1050 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
vg0910353994 NA 2.11E-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
vg0910353994 NA 8.32E-11 mr1128 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
vg0910353994 NA 4.57E-19 mr1164 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
vg0910353994 NA 6.53E-14 mr1205 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
vg0910353994 NA 2.01E-11 mr1272 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
vg0910353994 NA 6.62E-07 mr1338 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
vg0910353994 NA 1.29E-11 mr1454 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
vg0910353994 NA 1.78E-21 mr1580 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
vg0910353994 NA 8.34E-08 mr1604 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
vg0910353994 NA 5.40E-21 mr1627 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
vg0910353994 NA 3.67E-07 mr1668 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
vg0910353994 NA 4.05E-07 mr1680 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
vg0910353994 NA 5.44E-07 mr1779 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
vg0910353994 NA 3.90E-19 mr1825 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
vg0910353994 NA 7.88E-07 mr1886 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