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Detailed information for vg0618589804:

Variant ID: vg0618589804 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 18589804
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


ATCCATGAAGACTTCCATGATATCCTCGATCATGTCAGAGAAAATAGACATCATGCATCTTTGAAATGACGCGGGTGCATTGCACAACCCGAACGACATT[T/C]
TGCGATATGCATACGTTCCGTACGGGCACGTGAACGTGGTCTTACTTTGATCATCAGGATGGATGGGGATTTGATGATAACCAGAATACCCATCAAGGAA

Reverse complement sequence

TTCCTTGATGGGTATTCTGGTTATCATCAAATCCCCATCCATCCTGATGATCAAAGTAAGACCACGTTCACGTGCCCGTACGGAACGTATGCATATCGCA[A/G]
AATGTCGTTCGGGTTGTGCAATGCACCCGCGTCATTTCAAAGATGCATGATGTCTATTTTCTCTGACATGATCGAGGATATCATGGAAGTCTTCATGGAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.40% 0.30% 9.23% 56.09% NA
All Indica  2759 9.40% 0.40% 12.47% 77.71% NA
All Japonica  1512 86.20% 0.10% 2.12% 11.64% NA
Aus  269 3.00% 0.00% 15.61% 81.41% NA
Indica I  595 17.10% 0.00% 11.60% 71.26% NA
Indica II  465 10.50% 0.00% 2.37% 87.10% NA
Indica III  913 2.10% 1.20% 17.31% 79.41% NA
Indica Intermediate  786 11.30% 0.10% 13.49% 75.06% NA
Temperate Japonica  767 87.40% 0.10% 0.39% 12.13% NA
Tropical Japonica  504 84.70% 0.00% 4.96% 10.32% NA
Japonica Intermediate  241 85.50% 0.00% 1.66% 12.86% NA
VI/Aromatic  96 13.50% 0.00% 13.54% 72.92% NA
Intermediate  90 47.80% 0.00% 5.56% 46.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0618589804 T -> C LOC_Os06g31980.1 upstream_gene_variant ; 4814.0bp to feature; MODIFIER silent_mutation Average:14.445; most accessible tissue: Zhenshan97 panicle, score: 20.424 N N N N
vg0618589804 T -> C LOC_Os06g31990.1 intron_variant ; MODIFIER silent_mutation Average:14.445; most accessible tissue: Zhenshan97 panicle, score: 20.424 N N N N
vg0618589804 T -> DEL N N silent_mutation Average:14.445; most accessible tissue: Zhenshan97 panicle, score: 20.424 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0618589804 NA 7.62E-11 mr1172 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
vg0618589804 NA 8.67E-07 mr1245 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
vg0618589804 NA 8.35E-08 mr1354 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
vg0618589804 NA 1.77E-18 mr1518 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
vg0618589804 NA 2.47E-21 mr1676 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
vg0618589804 NA 1.62E-06 mr1681 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
vg0618589804 NA 5.53E-06 mr1686 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
vg0618589804 NA 9.29E-06 mr1043_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
vg0618589804 NA 7.20E-06 mr1167_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
vg0618589804 NA 1.18E-18 mr1239_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
vg0618589804 NA 6.52E-07 mr1269_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
vg0618589804 NA 3.52E-10 mr1282_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
vg0618589804 NA 3.70E-07 mr1479_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
vg0618589804 NA 4.02E-06 mr1479_2 Jap_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
vg0618589804 NA 1.06E-11 mr1667_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
vg0618589804 NA 9.57E-06 mr1677_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
vg0618589804 NA 1.32E-08 mr1681_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