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Detailed information for vg0704650445:

Variant ID: vg0704650445 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4650445
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TGGATGAGTTCATAGTGGCTGGAAACACATGTTCTGGTGCAGCAAGAGAACTCTCAACTGCTGGCCTAGTGGTGATGCTGCTTGGTCCCAACGTCAAACA[C/T]
TTGGTGGGCGTCATGTCGACACCGTTCCCGTTGAAAGGATGCACGTGCTGGACATCAAGCAGGTAACACCCATCATAGATGTTGCGTCCATTGGTGACAG

Reverse complement sequence

CTGTCACCAATGGACGCAACATCTATGATGGGTGTTACCTGCTTGATGTCCAGCACGTGCATCCTTTCAACGGGAACGGTGTCGACATGACGCCCACCAA[G/A]
TGTTTGACGTTGGGACCAAGCAGCATCACCACTAGGCCAGCAGTTGAGAGTTCTCTTGCTGCACCAGAACATGTGTTTCCAGCCACTATGAACTCATCCA

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 89.30% 10.70% 0.02% 0.00% NA
All Indica  2759 98.40% 1.60% 0.04% 0.00% NA
All Japonica  1512 89.10% 10.90% 0.00% 0.00% NA
Aus  269 25.70% 74.30% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 97.30% 2.70% 0.00% 0.00% NA
Temperate Japonica  767 92.00% 8.00% 0.00% 0.00% NA
Tropical Japonica  504 83.90% 16.10% 0.00% 0.00% NA
Japonica Intermediate  241 90.50% 9.50% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0704650445 C -> T LOC_Os07g08940.1 synonymous_variant ; p.Lys37Lys; LOW synonymous_codon Average:62.52; most accessible tissue: Zhenshan97 young leaf, score: 78.044 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0704650445 NA 1.74E-07 mr1057 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
vg0704650445 NA 5.15E-06 mr1100 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
vg0704650445 NA 2.47E-07 mr1613 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
vg0704650445 NA 5.92E-07 mr1962 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
vg0704650445 NA 1.28E-07 mr1057_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
vg0704650445 NA 5.62E-06 mr1522_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