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Detailed information for vg0709509554:

Variant ID: vg0709509554 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9509554
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, T: 0.38, others allele: 0.00, population size: 168. )

Flanking Sequence (100 bp) in Reference Genome:


TGCTTGCGACATAATCTGAGTACAAAAGTACCTATCAAGTTATGGAGTTCTATCTTCCTATGCTTTCCGTTTGGTTTGCCAATGGATGGTTGCCTTTGGG[T/C]
CGATTCCTAGCACCCGGGGGCTCGTTGGATGGACCAAGTAACGCAAGGTGCTAAGTATTATTCAGAATAAATCAAAAGCATAGGGATGAGATAAATTTAT

Reverse complement sequence

ATAAATTTATCTCATCCCTATGCTTTTGATTTATTCTGAATAATACTTAGCACCTTGCGTTACTTGGTCCATCCAACGAGCCCCCGGGTGCTAGGAATCG[A/G]
CCCAAAGGCAACCATCCATTGGCAAACCAAACGGAAAGCATAGGAAGATAGAACTCCATAACTTGATAGGTACTTTTGTACTCAGATTATGTCGCAAGCA

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 61.50% 31.30% 5.10% 2.09% NA
All Indica  2759 91.00% 3.00% 5.91% 0.00% NA
All Japonica  1512 11.80% 79.20% 2.45% 6.55% NA
Aus  269 38.70% 55.00% 6.32% 0.00% NA
Indica I  595 81.80% 2.40% 15.80% 0.00% NA
Indica II  465 95.30% 4.10% 0.65% 0.00% NA
Indica III  913 96.60% 1.30% 2.08% 0.00% NA
Indica Intermediate  786 89.10% 5.00% 5.98% 0.00% NA
Temperate Japonica  767 4.80% 80.30% 2.74% 12.13% NA
Tropical Japonica  504 16.50% 83.10% 0.40% 0.00% NA
Japonica Intermediate  241 24.50% 67.20% 5.81% 2.49% NA
VI/Aromatic  96 56.20% 22.90% 20.83% 0.00% NA
Intermediate  90 62.20% 33.30% 4.44% 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
vg0709509554 T -> DEL N N silent_mutation Average:31.996; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N
vg0709509554 T -> C LOC_Os07g16290.1 intron_variant ; MODIFIER silent_mutation Average:31.996; most accessible tissue: Zhenshan97 flower, score: 61.872 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709509554 NA 3.61E-06 mr1058 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
vg0709509554 NA 6.86E-16 mr1147 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
vg0709509554 NA 1.32E-07 mr1280 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
vg0709509554 NA 1.69E-06 mr1285 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
vg0709509554 NA 1.30E-09 mr1299 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
vg0709509554 NA 5.62E-08 mr1345 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
vg0709509554 NA 3.16E-14 mr1379 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
vg0709509554 NA 1.24E-09 mr1524 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
vg0709509554 NA 1.50E-08 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
vg0709509554 NA 7.72E-06 mr1652 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
vg0709509554 NA 1.56E-07 mr1756 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
vg0709509554 NA 4.61E-07 mr1761 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
vg0709509554 NA 6.00E-08 mr1763 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
vg0709509554 NA 7.71E-08 mr1788 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
vg0709509554 NA 8.98E-06 mr1875 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
vg0709509554 3.36E-06 NA mr1936 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
vg0709509554 NA 8.47E-06 mr1941 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
vg0709509554 NA 1.99E-06 mr1110_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