Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0435226987:

Variant ID: vg0435226987 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 35226987
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGGCCGCCGGGGGTGACGACAGGGTCATGGCGAATTTCTTTCCCATGGCCCTGAAGGGACAGGCGCGGGGTTGGCTAATGAACTTGCCACCCGTGTCC[G/A]
TCCACTCTTGGGAGGATTTGTGCCAACAGTTCACCATGAACTTTCAAGGCACATATCCGCGCCCAGGTGTAGAAGCGGACTTACATGCAGTCCAGCGATG

Reverse complement sequence

CATCGCTGGACTGCATGTAAGTCCGCTTCTACACCTGGGCGCGGATATGTGCCTTGAAAGTTCATGGTGAACTGTTGGCACAAATCCTCCCAAGAGTGGA[C/T]
GGACACGGGTGGCAAGTTCATTAGCCAACCCCGCGCCTGTCCCTTCAGGGCCATGGGAAAGAAATTCGCCATGACCCTGTCGTCACCCCCGGCGGCCTCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.40% 10.40% 3.96% 49.24% NA
All Indica  2759 8.80% 3.10% 5.91% 82.17% NA
All Japonica  1512 87.20% 10.50% 1.52% 0.73% NA
Aus  269 5.20% 86.20% 0.00% 8.55% NA
Indica I  595 6.70% 1.30% 4.71% 87.23% NA
Indica II  465 6.00% 0.20% 3.66% 90.11% NA
Indica III  913 8.40% 2.80% 8.00% 80.72% NA
Indica Intermediate  786 12.60% 6.40% 5.73% 75.32% NA
Temperate Japonica  767 99.60% 0.10% 0.13% 0.13% NA
Tropical Japonica  504 65.30% 31.00% 2.18% 1.59% NA
Japonica Intermediate  241 93.80% 0.80% 4.56% 0.83% NA
VI/Aromatic  96 82.30% 6.20% 1.04% 10.42% NA
Intermediate  90 72.20% 10.00% 0.00% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0435226987 G -> DEL LOC_Os04g59220.1 N frameshift_variant Average:10.405; most accessible tissue: Callus, score: 30.589 N N N N
vg0435226987 G -> A LOC_Os04g59220.1 missense_variant ; p.Val296Ile; MODERATE nonsynonymous_codon ; V296I Average:10.405; most accessible tissue: Callus, score: 30.589 benign 0.619 DELETERIOUS 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0435226987 NA 3.20E-06 mr1057 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
vg0435226987 NA 1.79E-07 mr1076 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
vg0435226987 NA 9.55E-08 mr1082 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
vg0435226987 NA 7.11E-07 mr1083 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
vg0435226987 NA 4.15E-06 mr1220 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
vg0435226987 NA 1.40E-07 mr1230 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
vg0435226987 NA 1.10E-06 mr1286 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
vg0435226987 NA 2.89E-06 mr1345 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
vg0435226987 NA 1.56E-07 mr1365 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
vg0435226987 NA 7.13E-06 mr1400 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
vg0435226987 NA 6.66E-06 mr1408 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
vg0435226987 NA 7.60E-07 mr1417 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
vg0435226987 NA 9.89E-06 mr1634 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
vg0435226987 NA 2.33E-07 mr1665 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
vg0435226987 NA 2.16E-10 mr1047_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
vg0435226987 3.29E-06 NA mr1104_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
vg0435226987 NA 2.46E-08 mr1220_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
vg0435226987 1.90E-06 NA mr1226_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
vg0435226987 NA 9.13E-06 mr1295_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
vg0435226987 NA 4.21E-06 mr1319_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
vg0435226987 NA 1.47E-14 mr1530_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
vg0435226987 NA 3.61E-06 mr1740_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
vg0435226987 NA 8.48E-06 mr1936_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