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Detailed information for vg0906350119:

Variant ID: vg0906350119 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6350119
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


AGATGTTGCAGGACACCAAGTAGGACTGCGAAAGTGAAAAGGGAGCCCATAAATTGGACAAGATGTTAGAGGACTACAGAACTTCGTTATACCCAGGTTG[C/T]
GAGCAGGGGCACAAAAAGTTGGATACCACTCTGGAGTTCTTGCAATGGAAGGCAAAAAATGGGGTTAGTGACAAGGCATTTGGCGATTTATTGAAACTCG

Reverse complement sequence

CGAGTTTCAATAAATCGCCAAATGCCTTGTCACTAACCCCATTTTTTGCCTTCCATTGCAAGAACTCCAGAGTGGTATCCAACTTTTTGTGCCCCTGCTC[G/A]
CAACCTGGGTATAACGAAGTTCTGTAGTCCTCTAACATCTTGTCCAATTTATGGGCTCCCTTTTCACTTTCGCAGTCCTACTTGGTGTCCTGCAACATCT

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 41.00% 21.10% 4.89% 32.99% NA
All Indica  2759 14.30% 30.90% 7.36% 47.48% NA
All Japonica  1512 95.90% 3.80% 0.07% 0.26% NA
Aus  269 9.70% 14.50% 7.43% 68.40% NA
Indica I  595 16.10% 15.30% 8.74% 59.83% NA
Indica II  465 8.00% 53.80% 3.23% 35.05% NA
Indica III  913 13.90% 25.60% 9.64% 50.82% NA
Indica Intermediate  786 17.00% 35.20% 6.11% 41.60% NA
Temperate Japonica  767 95.60% 4.30% 0.00% 0.13% NA
Tropical Japonica  504 99.00% 0.60% 0.00% 0.40% NA
Japonica Intermediate  241 90.50% 8.70% 0.41% 0.41% NA
VI/Aromatic  96 16.70% 36.50% 3.12% 43.75% NA
Intermediate  90 56.70% 17.80% 4.44% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0906350119 C -> DEL LOC_Os09g11400.1 N frameshift_variant Average:18.22; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0906350119 C -> T LOC_Os09g11400.1 synonymous_variant ; p.Cys43Cys; LOW synonymous_codon Average:18.22; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906350119 5.16E-07 2.36E-11 mr1757 Jap_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
vg0906350119 NA 3.32E-06 mr1169_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
vg0906350119 NA 1.38E-06 mr1295_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
vg0906350119 2.32E-06 2.76E-09 mr1549_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
vg0906350119 1.98E-06 2.42E-07 mr1550_2 Jap_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
vg0906350119 8.78E-08 1.34E-10 mr1757_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
vg0906350119 NA 1.43E-07 mr1842_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
vg0906350119 NA 1.94E-06 mr1933_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
vg0906350119 4.32E-06 4.32E-06 mr1954_2 Jap_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