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Detailed information for vg1125628490:

Variant ID: vg1125628490 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25628490
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, G: 0.21, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTTCACAAGTGCCGGAAGCAGGCAAATCTTTGGTGAAGGCCGAGCAAGCCACACCTAATCCAGCCAATCAGGATGACCATGAATTTACAAGTGCTATC[C/G]
AAGAAACCAAGGAAAAGATCGCACAAATCGGGGTAAAGATCGAGGAACGGCTTCTTATCGAATGCATAGTTGAGGAGATTAAAGAGCTTTTGGGAGGTAA

Reverse complement sequence

TTACCTCCCAAAAGCTCTTTAATCTCCTCAACTATGCATTCGATAAGAAGCCGTTCCTCGATCTTTACCCCGATTTGTGCGATCTTTTCCTTGGTTTCTT[G/C]
GATAGCACTTGTAAATTCATGGTCATCCTGATTGGCTGGATTAGGTGTGGCTTGCTCGGCCTTCACCAAAGATTTGCCTGCTTCCGGCACTTGTGAAGGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.10% 30.90% 0.74% 7.26% NA
All Indica  2759 66.60% 22.40% 1.05% 9.97% NA
All Japonica  1512 48.90% 46.60% 0.33% 4.17% NA
Aus  269 79.20% 20.80% 0.00% 0.00% NA
Indica I  595 93.60% 5.50% 0.34% 0.50% NA
Indica II  465 35.70% 58.70% 0.43% 5.16% NA
Indica III  913 63.60% 15.10% 1.10% 20.15% NA
Indica Intermediate  786 67.80% 22.10% 1.91% 8.14% NA
Temperate Japonica  767 74.70% 25.20% 0.13% 0.00% NA
Tropical Japonica  504 11.50% 76.00% 0.60% 11.90% NA
Japonica Intermediate  241 45.20% 53.10% 0.41% 1.24% NA
VI/Aromatic  96 44.80% 55.20% 0.00% 0.00% NA
Intermediate  90 58.90% 34.40% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125628490 C -> DEL LOC_Os11g42580.1 N frameshift_variant Average:58.834; most accessible tissue: Zhenshan97 flower, score: 73.141 N N N N
vg1125628490 C -> G LOC_Os11g42580.1 missense_variant ; p.Gln545Glu; MODERATE nonsynonymous_codon ; Q545E Average:58.834; most accessible tissue: Zhenshan97 flower, score: 73.141 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125628490 NA 8.98E-13 Grain_width Ind_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
vg1125628490 NA 4.86E-06 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
vg1125628490 NA 9.98E-11 mr1084 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
vg1125628490 2.24E-07 NA mr1133 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
vg1125628490 NA 9.89E-08 mr1133 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
vg1125628490 NA 7.47E-09 mr1192 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
vg1125628490 4.58E-08 2.35E-16 mr1205 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
vg1125628490 2.83E-06 1.28E-10 mr1206 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
vg1125628490 NA 4.64E-06 mr1209 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
vg1125628490 NA 8.89E-07 mr1229 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
vg1125628490 NA 7.22E-06 mr1297 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
vg1125628490 7.55E-06 8.15E-07 mr1367 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
vg1125628490 NA 8.74E-07 mr1644 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
vg1125628490 NA 1.53E-07 mr1668 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
vg1125628490 NA 5.74E-12 mr1775 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
vg1125628490 NA 1.58E-06 mr1820 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
vg1125628490 NA 1.64E-06 mr1835 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
vg1125628490 NA 9.65E-06 mr1858 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
vg1125628490 NA 9.69E-06 mr1859 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
vg1125628490 NA 7.52E-07 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
vg1125628490 NA 6.39E-06 mr1898 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
vg1125628490 NA 5.26E-08 mr1951 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
vg1125628490 NA 6.71E-06 mr1191_2 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
vg1125628490 NA 3.82E-06 mr1875_2 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
vg1125628490 NA 1.12E-06 mr1931_2 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