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Detailed information for vg0411404313:

Variant ID: vg0411404313 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 11404313
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.27, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


ATGAGCTTGCGCGTAGGAAGCTTGATCGGGAACAATTCTTTTTCTGCCAGTTGTGCTGACACCTGCCAACCTTCCTTCATGGCGAGACGTAGGAACTCCG[A/G]
TAGGATCAGTCTCGGCCACGTAATCGATACAAAACTCAATGGCTTCCTCGGTCGTGTCACCTTCAATGATGCTCCCCTCTGGTTTTGCTCTGTTCCGAAC

Reverse complement sequence

GTTCGGAACAGAGCAAAACCAGAGGGGAGCATCATTGAAGGTGACACGACCGAGGAAGCCATTGAGTTTTGTATCGATTACGTGGCCGAGACTGATCCTA[T/C]
CGGAGTTCCTACGTCTCGCCATGAAGGAAGGTTGGCAGGTGTCAGCACAACTGGCAGAAAAAGAATTGTTCCCGATCAAGCTTCCTACGCGCAAGCTCAT

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 53.80% 34.60% 2.64% 8.91% NA
All Indica  2759 52.10% 47.50% 0.25% 0.14% NA
All Japonica  1512 64.90% 0.90% 7.08% 27.12% NA
Aus  269 0.40% 99.60% 0.00% 0.00% NA
Indica I  595 77.10% 22.90% 0.00% 0.00% NA
Indica II  465 47.70% 51.40% 0.22% 0.65% NA
Indica III  913 41.90% 57.70% 0.33% 0.00% NA
Indica Intermediate  786 47.50% 52.00% 0.38% 0.13% NA
Temperate Japonica  767 93.50% 0.30% 0.91% 5.35% NA
Tropical Japonica  504 16.90% 1.60% 18.06% 63.49% NA
Japonica Intermediate  241 74.30% 1.70% 3.73% 20.33% NA
VI/Aromatic  96 80.20% 13.50% 3.12% 3.12% NA
Intermediate  90 53.30% 33.30% 8.89% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0411404313 A -> DEL LOC_Os04g20390.1 N frameshift_variant Average:25.922; most accessible tissue: Minghui63 root, score: 33.152 N N N N
vg0411404313 A -> G LOC_Os04g20390.1 missense_variant ; p.Ile563Thr; MODERATE nonsynonymous_codon ; I563T Average:25.922; most accessible tissue: Minghui63 root, score: 33.152 benign 1.473 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0411404313 NA 6.85E-06 mr1304 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
vg0411404313 NA 3.38E-13 mr1386 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
vg0411404313 NA 2.17E-06 mr1386 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
vg0411404313 NA 8.68E-09 mr1403 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
vg0411404313 NA 3.28E-07 mr1403 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
vg0411404313 NA 1.27E-07 mr1414 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
vg0411404313 NA 1.33E-16 mr1830 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
vg0411404313 NA 1.12E-08 mr1830 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
vg0411404313 3.25E-08 2.89E-26 mr1846 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
vg0411404313 5.00E-07 7.86E-15 mr1846 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
vg0411404313 NA 1.66E-07 mr1304_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
vg0411404313 NA 1.59E-07 mr1607_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
vg0411404313 NA 1.58E-06 mr1608_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
vg0411404313 9.01E-09 1.89E-21 mr1830_2 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
vg0411404313 4.64E-08 1.23E-16 mr1830_2 Ind_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
vg0411404313 1.89E-16 6.78E-54 mr1846_2 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
vg0411404313 3.29E-14 3.66E-33 mr1846_2 Ind_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