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Detailed information for vg0317064370:

Variant ID: vg0317064370 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17064370
Reference Allele: AAlternative Allele: G,C
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: 182. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTGCTAACCTTGAAAAGTGCATCTTTTGCACGGAACGAGTTTCATTTCTTGGATATATTGTTACTCCACAGGGAATTGAGGTGGATGAGATGAAAATT[A/G,C]
AAGCCATAAAGAGTTGGCCGGTTCCCCAAACCATCACACAGGTGAGGAGTTTTCTTGGTCTTGCAGGATTCTATCATCGTTTCGTCAAAGATTTTAGTAC

Reverse complement sequence

GTACTAAAATCTTTGACGAAACGATGATAGAATCCTGCAAGACCAAGAAAACTCCTCACCTGTGTGATGGTTTGGGGAACCGGCCAACTCTTTATGGCTT[T/C,G]
AATTTTCATCTCATCCACCTCAATTCCCTGTGGAGTAACAATATATCCAAGAAATGAAACTCGTTCCGTGCAAAAGATGCACTTTTCAAGGTTAGCAAAC

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 61.10% 28.10% 4.93% 5.82% C: 0.02%
All Indica  2759 88.50% 7.40% 1.52% 2.57% C: 0.04%
All Japonica  1512 4.10% 70.60% 11.97% 13.36% NA
Aus  269 94.40% 5.20% 0.37% 0.00% NA
Indica I  595 97.80% 1.70% 0.50% 0.00% NA
Indica II  465 85.80% 6.50% 3.01% 4.73% NA
Indica III  913 80.90% 13.30% 1.31% 4.38% C: 0.11%
Indica Intermediate  786 91.70% 5.50% 1.65% 1.15% NA
Temperate Japonica  767 0.30% 66.90% 15.38% 17.47% NA
Tropical Japonica  504 11.30% 77.20% 6.35% 5.16% NA
Japonica Intermediate  241 1.20% 68.50% 12.86% 17.43% NA
VI/Aromatic  96 83.30% 15.60% 1.04% 0.00% NA
Intermediate  90 57.80% 31.10% 8.89% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0317064370 A -> C LOC_Os03g29940.1 missense_variant ; p.Lys733Gln; MODERATE nonsynonymous_codon ; K733Q Average:30.314; most accessible tissue: Minghui63 flag leaf, score: 53.617 benign 0.968 TOLERATED 0.08
vg0317064370 A -> DEL LOC_Os03g29940.1 N frameshift_variant Average:30.314; most accessible tissue: Minghui63 flag leaf, score: 53.617 N N N N
vg0317064370 A -> G LOC_Os03g29940.1 missense_variant ; p.Lys733Glu; MODERATE nonsynonymous_codon ; K733E Average:30.314; most accessible tissue: Minghui63 flag leaf, score: 53.617 benign 0.498 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317064370 1.10E-06 NA mr1038_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
vg0317064370 2.04E-06 NA mr1038_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
vg0317064370 1.21E-06 NA mr1141_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
vg0317064370 7.01E-06 NA mr1141_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
vg0317064370 NA 2.98E-09 mr1299_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
vg0317064370 NA 9.27E-07 mr1358_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
vg0317064370 NA 8.82E-12 mr1377_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
vg0317064370 8.96E-06 NA mr1389_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
vg0317064370 NA 6.72E-06 mr1391_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
vg0317064370 NA 9.92E-18 mr1416_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
vg0317064370 NA 3.85E-25 mr1484_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
vg0317064370 NA 5.11E-19 mr1637_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
vg0317064370 NA 2.71E-08 mr1700_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
vg0317064370 NA 7.13E-07 mr1727_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
vg0317064370 NA 1.80E-06 mr1785_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
vg0317064370 NA 2.18E-07 mr1804_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
vg0317064370 NA 2.35E-08 mr1837_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
vg0317064370 NA 6.12E-14 mr1938_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
vg0317064370 NA 4.85E-21 mr1945_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