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Detailed information for vg0328939602:

Variant ID: vg0328939602 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 28939602
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.01, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTAACATACTCAAGGCAGCAGAAGAACAAGTTAAGCTGATACGAGAACGTTTAAAGACAGCTCAGAACCGTCAAAAGAATTACGCTGACAATCGGAGG[C/T,A]
GAGATCTTGAGTTCGAAAAAGGAGACCATGTGTACCTGCGGGTATCACCTCTCCGTGGTATGAGGAAGTTTGGGATGTCCGGCAAGTTAGCGCCCCGCTA

Reverse complement sequence

TAGCGGGGCGCTAACTTGCCGGACATCCCAAACTTCCTCATACCACGGAGAGGTGATACCCGCAGGTACACATGGTCTCCTTTTTCGAACTCAAGATCTC[G/A,T]
CCTCCGATTGTCAGCGTAATTCTTTTGACGGTTCTGAGCTGTCTTTAAACGTTCTCGTATCAGCTTAACTTGTTCTTCTGCTGCCTTGAGTATGTTAGGA

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 79.50% 17.10% 2.92% 0.38% A: 0.02%
All Indica  2759 69.80% 28.40% 1.12% 0.65% A: 0.04%
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 61.00% 1.10% 37.92% 0.00% NA
Indica I  595 90.90% 9.10% 0.00% 0.00% NA
Indica II  465 45.40% 49.70% 3.23% 1.72% NA
Indica III  913 67.80% 31.50% 0.33% 0.33% NA
Indica Intermediate  786 70.50% 26.80% 1.65% 0.89% A: 0.13%
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 1.00% 2.08% 0.00% NA
Intermediate  90 80.00% 16.70% 3.33% 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
vg0328939602 C -> T LOC_Os03g50670.1 stop_gained ; p.Arg1305*; HIGH stop_gained Average:24.335; most accessible tissue: Zhenshan97 root, score: 39.742 N N N N
vg0328939602 C -> A LOC_Os03g50670.1 synonymous_variant ; p.Arg1305Arg; LOW synonymous_codon Average:24.335; most accessible tissue: Zhenshan97 root, score: 39.742 N N N N
vg0328939602 C -> DEL LOC_Os03g50670.1 N frameshift_variant Average:24.335; most accessible tissue: Zhenshan97 root, score: 39.742 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0328939602 NA 4.91E-07 mr1003 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
vg0328939602 NA 8.59E-06 mr1006 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
vg0328939602 NA 1.83E-06 mr1030 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
vg0328939602 9.55E-06 4.62E-08 mr1051 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
vg0328939602 NA 9.17E-06 mr1052 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
vg0328939602 NA 9.58E-06 mr1192 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
vg0328939602 NA 1.89E-06 mr1241 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
vg0328939602 6.69E-06 6.69E-06 mr1294 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
vg0328939602 NA 9.42E-06 mr1297 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
vg0328939602 7.03E-06 7.03E-06 mr1302 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
vg0328939602 NA 3.10E-06 mr1439 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
vg0328939602 2.08E-06 2.08E-06 mr1470 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
vg0328939602 1.45E-06 1.45E-06 mr1488 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
vg0328939602 1.40E-06 1.40E-06 mr1507 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
vg0328939602 NA 1.60E-07 mr1536 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
vg0328939602 NA 5.36E-06 mr1537 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
vg0328939602 5.94E-06 5.94E-06 mr1832 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
vg0328939602 NA 1.36E-07 mr1931 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
vg0328939602 NA 9.10E-06 mr1931 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
vg0328939602 NA 9.54E-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
vg0328939602 NA 2.46E-06 mr1958 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
vg0328939602 NA 2.90E-06 mr1974 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