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Detailed information for vg1016551649:

Variant ID: vg1016551649 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 16551649
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.15, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


AACTTCGGCAAGATCTCTCTCCTTGACTCGGAGTCGGACCAGTCGGGAGAGAACTGGATCTCAGTCCCGTTTGGACTCCCAAACGCGGCTGAAAGTTACT[C/T]
CAAGACCATCTCAATCGAGTCGGCTTCAAACCACTCGGCTGAGATTGCATCTTCTCCAACGTCACCAGATCAAGATGATGGGGCTTACCCACCGATCCTG

Reverse complement sequence

CAGGATCGGTGGGTAAGCCCCATCATCTTGATCTGGTGACGTTGGAGAAGATGCAATCTCAGCCGAGTGGTTTGAAGCCGACTCGATTGAGATGGTCTTG[G/A]
AGTAACTTTCAGCCGCGTTTGGGAGTCCAAACGGGACTGAGATCCAGTTCTCTCCCGACTGGTCCGACTCCGAGTCAAGGAGAGAGATCTTGCCGAAGTT

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 20.50% 2.30% 38.28% 38.93% NA
All Indica  2759 12.20% 1.20% 41.61% 44.94% NA
All Japonica  1512 40.10% 4.00% 29.70% 26.26% NA
Aus  269 0.00% 2.20% 37.17% 60.59% NA
Indica I  595 2.70% 3.90% 36.13% 57.31% NA
Indica II  465 14.80% 0.00% 23.66% 61.51% NA
Indica III  913 15.90% 0.30% 56.08% 27.71% NA
Indica Intermediate  786 13.60% 1.00% 39.57% 45.80% NA
Temperate Japonica  767 73.80% 0.10% 10.95% 15.12% NA
Tropical Japonica  504 2.40% 10.10% 47.22% 40.28% NA
Japonica Intermediate  241 11.60% 3.30% 52.70% 32.37% NA
VI/Aromatic  96 1.00% 5.20% 73.96% 19.79% NA
Intermediate  90 26.70% 4.40% 45.56% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1016551649 C -> T LOC_Os10g31590.1 missense_variant ; p.Ser62Phe; MODERATE nonsynonymous_codon ; S62F Average:26.974; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 benign -0.483 TOLERATED 0.06
vg1016551649 C -> DEL LOC_Os10g31590.1 N frameshift_variant Average:26.974; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1016551649 NA 3.20E-13 Grain_length 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
vg1016551649 NA 9.01E-15 Grain_length 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
vg1016551649 NA 9.54E-06 mr1029 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
vg1016551649 NA 7.13E-09 mr1137 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
vg1016551649 NA 3.46E-06 mr1330 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
vg1016551649 NA 4.73E-37 mr1486 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
vg1016551649 NA 1.28E-14 mr1486 Jap_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
vg1016551649 NA 5.74E-07 mr1530 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
vg1016551649 NA 4.24E-06 mr1548 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
vg1016551649 NA 4.12E-07 mr1617 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
vg1016551649 NA 5.78E-06 mr1826 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
vg1016551649 NA 1.58E-06 mr1871 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
vg1016551649 NA 9.99E-12 mr1902 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
vg1016551649 NA 3.55E-06 mr1902 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
vg1016551649 NA 9.86E-07 mr1570_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