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Detailed information for vg0410821067:

Variant ID: vg0410821067 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10821067
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


TCAAACTGGTTGAACCTAGGAGCATACTGAGGCTGAGGCGATCCCCCCTGTTGATAGTGAACATGAGGTGAAGGGGGCTGGTATTGATAATTCAAGTTAC[T/C]
CCCTTGGTAGTTCTGGACATTCGGCTGAATATTACGCACTAACTGCTCAGGGATAACTTGGGCAGCAACCGATTGTCCGGTTGTACAACGTGTACCAGAT

Reverse complement sequence

ATCTGGTACACGTTGTACAACCGGACAATCGGTTGCTGCCCAAGTTATCCCTGAGCAGTTAGTGCGTAATATTCAGCCGAATGTCCAGAACTACCAAGGG[A/G]
GTAACTTGAATTATCAATACCAGCCCCCTTCACCTCATGTTCACTATCAACAGGGGGGATCGCCTCAGCCTCAGTATGCTCCTAGGTTCAACCAGTTTGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 23.60% 15.10% 1.02% 60.33% NA
All Indica  2759 6.00% 0.90% 1.38% 91.77% NA
All Japonica  1512 60.80% 38.20% 0.00% 0.93% NA
Aus  269 1.10% 0.00% 3.35% 95.54% NA
Indica I  595 2.20% 0.20% 0.84% 96.81% NA
Indica II  465 23.00% 1.70% 2.15% 73.12% NA
Indica III  913 1.00% 0.40% 0.99% 97.59% NA
Indica Intermediate  786 4.60% 1.40% 1.78% 92.24% NA
Temperate Japonica  767 95.80% 3.70% 0.00% 0.52% NA
Tropical Japonica  504 4.00% 94.80% 0.00% 1.19% NA
Japonica Intermediate  241 68.50% 29.90% 0.00% 1.66% NA
VI/Aromatic  96 1.00% 85.40% 0.00% 13.54% NA
Intermediate  90 26.70% 33.30% 1.11% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0410821067 T -> C LOC_Os04g19420.1 missense_variant ; p.Ser292Gly; MODERATE nonsynonymous_codon ; S292G Average:19.024; most accessible tissue: Callus, score: 53.381 possibly damaging -1.975 TOLERATED 1.00
vg0410821067 T -> DEL LOC_Os04g19420.1 N frameshift_variant Average:19.024; most accessible tissue: Callus, score: 53.381 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410821067 NA 3.82E-06 mr1045 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
vg0410821067 NA 2.17E-06 mr1090 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
vg0410821067 NA 3.42E-06 mr1121 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
vg0410821067 NA 9.29E-08 mr1194 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
vg0410821067 NA 4.91E-07 mr1206 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
vg0410821067 NA 5.73E-07 mr1403 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
vg0410821067 NA 3.88E-11 mr1454 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
vg0410821067 5.08E-08 5.07E-08 mr1703 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
vg0410821067 NA 1.54E-10 mr1712 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
vg0410821067 NA 3.67E-07 mr1715 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
vg0410821067 NA 3.57E-07 mr1739 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
vg0410821067 NA 3.46E-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
vg0410821067 NA 2.12E-09 mr1880 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
vg0410821067 NA 4.96E-08 mr1977 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
vg0410821067 NA 4.24E-06 mr1826_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