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Detailed information for vg0421077205:

Variant ID: vg0421077205 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21077205
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, G: 0.25, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


ACTAGTGTGGGATGTGCGATCGACATTGCAACACCCTCCATACTTGATCATTCCCTGTTGCTACGAAGAGCACACCATCATGGATGCCGTCGAGAGGCCC[A/G]
GGCTTGGTATCTTTTGCGGTGCCAATCTGATGTGTCCTGGTTGAAAAGATTGAATCTAAACGATTAGATCATTTCAATATAATAATACACGTAGACCATC

Reverse complement sequence

GATGGTCTACGTGTATTATTATATTGAAATGATCTAATCGTTTAGATTCAATCTTTTCAACCAGGACACATCAGATTGGCACCGCAAAAGATACCAAGCC[T/C]
GGGCCTCTCGACGGCATCCATGATGGTGTGCTCTTCGTAGCAACAGGGAATGATCAAGTATGGAGGGTGTTGCAATGTCGATCGCACATCCCACACTAGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.90% 20.00% 0.08% 0.04% NA
All Indica  2759 68.90% 30.90% 0.11% 0.07% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 71.70% 28.30% 0.00% 0.00% NA
Indica I  595 93.30% 6.70% 0.00% 0.00% NA
Indica II  465 73.10% 26.50% 0.43% 0.00% NA
Indica III  913 60.20% 39.50% 0.11% 0.11% NA
Indica Intermediate  786 58.10% 41.70% 0.00% 0.13% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 86.70% 12.20% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0421077205 A -> DEL LOC_Os04g34780.1 N frameshift_variant Average:49.643; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N
vg0421077205 A -> G LOC_Os04g34780.1 synonymous_variant ; p.Pro32Pro; LOW synonymous_codon Average:49.643; most accessible tissue: Minghui63 panicle, score: 76.913 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421077205 NA 7.13E-10 Heading_date 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
vg0421077205 NA 3.35E-09 mr1067 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
vg0421077205 NA 6.88E-06 mr1072 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
vg0421077205 NA 7.92E-08 mr1124 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
vg0421077205 NA 3.73E-07 mr1202 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
vg0421077205 3.14E-06 NA mr1592 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
vg0421077205 NA 7.70E-07 mr1592 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
vg0421077205 NA 3.55E-09 mr1861 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
vg0421077205 NA 1.86E-06 mr1074_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
vg0421077205 NA 1.92E-08 mr1124_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