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Detailed information for vg1000754606:

Variant ID: vg1000754606 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 754606
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.33, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


ATTGTCAGAATCGGTTGTATCGGCTTACCCAGTCTGACTCGGACCCAGCCGATCCTGATCGTAGCCGATCCGGACTCCAGCTGATTCTTGCTCTGTTCTC[A/G]
AATCAATCTCCACCTTTGATTCTGCTTTGTTCTTATCCTCATCTCCGATACTGATATAACCAAATTTGGTTGTTAACACCCGCCCGCTGCTTCTCCTTTT

Reverse complement sequence

AAAAGGAGAAGCAGCGGGCGGGTGTTAACAACCAAATTTGGTTATATCAGTATCGGAGATGAGGATAAGAACAAAGCAGAATCAAAGGTGGAGATTGATT[T/C]
GAGAACAGAGCAAGAATCAGCTGGAGTCCGGATCGGCTACGATCAGGATCGGCTGGGTCCGAGTCAGACTGGGTAAGCCGATACAACCGATTCTGACAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.50% 16.40% 1.71% 42.47% NA
All Indica  2759 52.80% 0.50% 0.47% 46.18% NA
All Japonica  1512 8.60% 48.70% 0.07% 42.66% NA
Aus  269 57.20% 0.70% 24.16% 17.84% NA
Indica I  595 63.00% 0.70% 0.34% 35.97% NA
Indica II  465 24.50% 0.60% 0.22% 74.62% NA
Indica III  913 55.00% 0.10% 0.22% 44.69% NA
Indica Intermediate  786 59.40% 0.80% 1.02% 38.80% NA
Temperate Japonica  767 9.90% 78.20% 0.13% 11.73% NA
Tropical Japonica  504 3.80% 5.60% 0.00% 90.67% NA
Japonica Intermediate  241 14.50% 44.80% 0.00% 40.66% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 36.70% 16.70% 2.22% 44.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000754606 A -> G LOC_Os10g02200.1 missense_variant ; p.Leu57Ser; MODERATE nonsynonymous_codon ; L57S Average:23.511; most accessible tissue: Zhenshan97 flag leaf, score: 49.845 unknown unknown TOLERATED 0.13
vg1000754606 A -> DEL LOC_Os10g02200.1 N frameshift_variant Average:23.511; most accessible tissue: Zhenshan97 flag leaf, score: 49.845 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000754606 NA 6.46E-07 mr1028 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
vg1000754606 NA 2.27E-06 mr1050 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
vg1000754606 NA 2.32E-07 mr1190 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
vg1000754606 NA 7.70E-07 mr1272 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
vg1000754606 1.52E-08 NA mr1310 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
vg1000754606 NA 2.11E-08 mr1369 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
vg1000754606 NA 6.47E-06 mr1433 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
vg1000754606 NA 3.17E-08 mr1453 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
vg1000754606 NA 6.53E-10 mr1498 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
vg1000754606 NA 1.11E-06 mr1652 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
vg1000754606 NA 3.10E-07 mr1680 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
vg1000754606 NA 2.78E-06 mr1887 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
vg1000754606 NA 9.77E-06 mr1887 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
vg1000754606 7.28E-09 NA mr1926 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
vg1000754606 2.23E-06 6.79E-08 mr1926 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
vg1000754606 NA 3.14E-06 mr1958 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
vg1000754606 NA 1.10E-09 mr1959 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
vg1000754606 3.10E-07 NA mr1310_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
vg1000754606 1.84E-06 2.58E-08 mr1310_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
vg1000754606 NA 5.22E-06 mr1959_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