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Detailed information for vg1004374773:

Variant ID: vg1004374773 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4374773
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TTACTGGATTAGATGTAACTTCATCGGCTAACCCTATGAGTATGAACGCCAAGAATCAATTTGACTTCAAGACCAAAAGCATAGGTGGCTGGTCTGGCTA[T/C]
GTGGCGGCATATATGGGCCAAGGGTCTGTTACCCCTCGAGAGCATGTAGCTTTCTTGGTCATGTGGCTGGAAAAGTTCCTCTTTTGTGGATCCAGTTGTG

Reverse complement sequence

CACAACTGGATCCACAAAAGAGGAACTTTTCCAGCCACATGACCAAGAAAGCTACATGCTCTCGAGGGGTAACAGACCCTTGGCCCATATATGCCGCCAC[A/G]
TAGCCAGACCAGCCACCTATGCTTTTGGTCTTGAAGTCAAATTGATTCTTGGCGTTCATACTCATAGGGTTAGCCGATGAAGTTACATCTAATCCAGTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.70% 14.70% 1.06% 27.47% NA
All Indica  2759 46.50% 24.30% 1.23% 27.98% NA
All Japonica  1512 68.60% 0.90% 0.46% 30.03% NA
Aus  269 94.80% 0.40% 0.00% 4.83% NA
Indica I  595 79.00% 6.10% 0.84% 14.12% NA
Indica II  465 46.90% 7.50% 0.86% 44.73% NA
Indica III  913 24.60% 47.30% 1.42% 26.62% NA
Indica Intermediate  786 47.10% 21.20% 1.53% 30.15% NA
Temperate Japonica  767 89.30% 0.10% 0.65% 9.91% NA
Tropical Japonica  504 34.70% 0.60% 0.20% 64.48% NA
Japonica Intermediate  241 73.40% 4.10% 0.41% 21.99% NA
VI/Aromatic  96 52.10% 2.10% 7.29% 38.54% NA
Intermediate  90 62.20% 11.10% 2.22% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004374773 T -> C LOC_Os10g08080.1 synonymous_variant ; p.Tyr166Tyr; LOW synonymous_codon Average:39.772; most accessible tissue: Zhenshan97 flag leaf, score: 67.31 N N N N
vg1004374773 T -> DEL LOC_Os10g08080.1 N frameshift_variant Average:39.772; most accessible tissue: Zhenshan97 flag leaf, score: 67.31 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004374773 NA 4.54E-07 mr1066 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
vg1004374773 NA 5.61E-06 mr1106 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
vg1004374773 NA 9.02E-06 mr1407 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
vg1004374773 8.66E-08 2.03E-06 mr1568 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
vg1004374773 4.49E-07 4.49E-07 mr1568 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
vg1004374773 2.93E-06 NA mr1631 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
vg1004374773 NA 5.44E-07 mr1631 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
vg1004374773 NA 8.89E-06 mr1908_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