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Detailed information for vg0406362113:

Variant ID: vg0406362113 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 6362113
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.08, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GGCGCCTGGGCAGCGTTGACGAAGTCGAACTGCGGTCCTTGATTCCACAGCGAAACTCCCAAGCCCGGCTGAATCGGTGGCAACCAATTAGGCGCACCTT[G/A]
ACTTGTATTCCCCTCCGGGTGAGCCGATGGGGTTGTACTTGAAATGCAGTGGGGTTGGTTGAGTTGCTGAAGGAAAGCTTGGAGTTGCGCCTGCAGAGCC

Reverse complement sequence

GGCTCTGCAGGCGCAACTCCAAGCTTTCCTTCAGCAACTCAACCAACCCCACTGCATTTCAAGTACAACCCCATCGGCTCACCCGGAGGGGAATACAAGT[C/T]
AAGGTGCGCCTAATTGGTTGCCACCGATTCAGCCGGGCTTGGGAGTTTCGCTGTGGAATCAAGGACCGCAGTTCGACTTCGTCAACGCTGCCCAGGCGCC

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 84.10% 11.60% 4.23% 0.00% NA
All Indica  2759 82.50% 11.30% 6.20% 0.00% NA
All Japonica  1512 95.20% 3.00% 1.85% 0.00% NA
Aus  269 61.70% 38.30% 0.00% 0.00% NA
Indica I  595 91.60% 7.70% 0.67% 0.00% NA
Indica II  465 84.30% 3.20% 12.47% 0.00% NA
Indica III  913 74.00% 16.00% 9.97% 0.00% NA
Indica Intermediate  786 84.20% 13.50% 2.29% 0.00% NA
Temperate Japonica  767 95.70% 4.30% 0.00% 0.00% NA
Tropical Japonica  504 95.40% 0.40% 4.17% 0.00% NA
Japonica Intermediate  241 92.90% 4.10% 2.90% 0.00% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 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
vg0406362113 G -> A LOC_Os04g11620.1 N stop_gained Average:49.605; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 N N N N
vg0406362113 G -> A LOC_Os04g11620.1 N nonsynonymous_codon ; Q333L Average:49.605; most accessible tissue: Zhenshan97 flag leaf, score: 76.356 possibly damaging 1.777 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0406362113 9.36E-10 2.10E-14 mr1071 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
vg0406362113 1.41E-07 4.23E-12 mr1080 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
vg0406362113 6.83E-08 9.57E-13 mr1100 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
vg0406362113 4.29E-10 7.49E-16 mr1140 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
vg0406362113 1.06E-08 1.51E-13 mr1203 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
vg0406362113 1.71E-08 3.93E-13 mr1395 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
vg0406362113 5.41E-11 4.88E-18 mr1613 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
vg0406362113 2.37E-09 6.58E-14 mr1618 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
vg0406362113 5.78E-08 6.51E-12 mr1619 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
vg0406362113 3.47E-08 3.68E-18 mr1913 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
vg0406362113 NA 7.06E-08 mr1962 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
vg0406362113 2.65E-11 NA mr1071_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
vg0406362113 1.50E-16 2.71E-23 mr1071_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
vg0406362113 2.47E-10 NA mr1080_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
vg0406362113 2.11E-14 1.74E-20 mr1080_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
vg0406362113 1.02E-07 NA mr1100_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
vg0406362113 4.37E-12 2.35E-19 mr1100_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
vg0406362113 1.01E-11 NA mr1203_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
vg0406362113 6.57E-16 8.39E-23 mr1203_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
vg0406362113 2.29E-10 9.41E-15 mr1402_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
vg0406362113 4.08E-12 NA mr1613_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
vg0406362113 1.20E-24 3.07E-37 mr1613_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
vg0406362113 2.36E-08 NA mr1619_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
vg0406362113 1.51E-16 1.81E-21 mr1619_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
vg0406362113 1.77E-10 3.48E-15 mr1795_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
vg0406362113 5.80E-07 NA mr1913_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
vg0406362113 4.81E-17 7.24E-28 mr1913_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
vg0406362113 2.41E-06 NA mr1962_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
vg0406362113 8.25E-16 8.76E-25 mr1962_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