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Detailed information for vg0728250650:

Variant ID: vg0728250650 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 28250650
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


GTATGTGCATCAAAACTGCCTGCTGCCTTTGCCTGACCCTGATCTCTGTTTCTCATGGGCATCAAGCTTGACACTGGACTTGTGATATATATCAGCTTCA[C/T]
TGTTATTTTGTCCATTATGCAAGGCCAGCAGTTCTGGAACATCTAGACCATCATTCCTTCCAGAGCTACTGCCACTGCCATAACCTTCACTGTGATCCTG

Reverse complement sequence

CAGGATCACAGTGAAGGTTATGGCAGTGGCAGTAGCTCTGGAAGGAATGATGGTCTAGATGTTCCAGAACTGCTGGCCTTGCATAATGGACAAAATAACA[G/A]
TGAAGCTGATATATATCACAAGTCCAGTGTCAAGCTTGATGCCCATGAGAAACAGAGATCAGGGTCAGGCAAAGGCAGCAGGCAGTTTTGATGCACATAC

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 54.80% 44.50% 0.06% 0.70% NA
All Indica  2759 46.60% 52.40% 0.04% 0.98% NA
All Japonica  1512 67.90% 31.70% 0.07% 0.26% NA
Aus  269 50.60% 49.40% 0.00% 0.00% NA
Indica I  595 58.50% 41.00% 0.00% 0.50% NA
Indica II  465 28.00% 70.80% 0.00% 1.29% NA
Indica III  913 54.00% 44.90% 0.00% 1.10% NA
Indica Intermediate  786 39.90% 58.90% 0.13% 1.02% NA
Temperate Japonica  767 96.50% 3.50% 0.00% 0.00% NA
Tropical Japonica  504 22.20% 77.20% 0.00% 0.60% NA
Japonica Intermediate  241 72.60% 26.60% 0.41% 0.41% NA
VI/Aromatic  96 79.20% 19.80% 1.04% 0.00% NA
Intermediate  90 71.10% 26.70% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0728250650 C -> DEL LOC_Os07g47270.1 N frameshift_variant Average:61.341; most accessible tissue: Zhenshan97 young leaf, score: 78.044 N N N N
vg0728250650 C -> T LOC_Os07g47270.1 missense_variant ; p.Ser450Asn; MODERATE nonsynonymous_codon ; S450N Average:61.341; most accessible tissue: Zhenshan97 young leaf, score: 78.044 benign 0.015 TOLERATED 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0728250650 NA 7.06E-12 Grain_width Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0728250650 NA 6.37E-06 mr1077 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
vg0728250650 NA 4.96E-07 mr1124 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
vg0728250650 NA 4.62E-07 mr1277 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
vg0728250650 NA 9.20E-08 mr1551 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
vg0728250650 NA 1.62E-06 mr1671 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
vg0728250650 NA 5.00E-13 mr1789 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
vg0728250650 NA 5.29E-14 mr1879 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
vg0728250650 NA 4.08E-10 mr1304_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
vg0728250650 NA 8.36E-08 mr1308_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
vg0728250650 NA 3.60E-07 mr1347_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
vg0728250650 NA 8.23E-10 mr1361_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
vg0728250650 NA 2.58E-13 mr1368_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
vg0728250650 NA 2.73E-07 mr1401_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
vg0728250650 NA 5.19E-15 mr1540_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
vg0728250650 NA 1.19E-07 mr1551_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
vg0728250650 NA 4.39E-11 mr1584_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
vg0728250650 NA 1.62E-06 mr1730_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
vg0728250650 NA 1.12E-14 mr1732_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
vg0728250650 NA 9.65E-06 mr1853_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
vg0728250650 NA 1.47E-06 mr1866_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
vg0728250650 NA 1.23E-10 mr1879_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
vg0728250650 NA 7.02E-10 mr1942_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