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Detailed information for vg0315006256:

Variant ID: vg0315006256 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15006256
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


TGAATCTGGAGTCCGAGATCTCGTCATTTGAATCTGTTTTGGTAGTCCACGGGCAGATTAAGGGTCTTGCCTGATTTCACAAAGGTAACTGATTTGGTAC[A/G]
TTTGAGTCGTTTTGGTTAATCGGCTTGCTCGAGTTTGCCAGTTGTCAATAGTTCGTTTATGTGAATTAATAATCACAGTAGTCGTGCTTGACGTGGAAAT

Reverse complement sequence

ATTTCCACGTCAAGCACGACTACTGTGATTATTAATTCACATAAACGAACTATTGACAACTGGCAAACTCGAGCAAGCCGATTAACCAAAACGACTCAAA[T/C]
GTACCAAATCAGTTACCTTTGTGAAATCAGGCAAGACCCTTAATCTGCCCGTGGACTACCAAAACAGATTCAAATGACGAGATCTCGGACTCCAGATTCA

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 58.10% 41.50% 0.40% 0.00% NA
All Indica  2759 70.60% 28.80% 0.54% 0.00% NA
All Japonica  1512 43.30% 56.50% 0.13% 0.00% NA
Aus  269 1.50% 98.10% 0.37% 0.00% NA
Indica I  595 46.10% 53.60% 0.34% 0.00% NA
Indica II  465 50.80% 48.40% 0.86% 0.00% NA
Indica III  913 89.20% 10.60% 0.22% 0.00% NA
Indica Intermediate  786 79.50% 19.60% 0.89% 0.00% NA
Temperate Japonica  767 17.50% 82.40% 0.13% 0.00% NA
Tropical Japonica  504 64.30% 35.50% 0.20% 0.00% NA
Japonica Intermediate  241 81.70% 18.30% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 7.30% 1.04% 0.00% NA
Intermediate  90 57.80% 42.20% 0.00% 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
vg0315006256 A -> G LOC_Os03g26220.1 upstream_gene_variant ; 1693.0bp to feature; MODIFIER silent_mutation Average:63.995; most accessible tissue: Callus, score: 83.362 N N N N
vg0315006256 A -> G LOC_Os03g26250.1 upstream_gene_variant ; 4906.0bp to feature; MODIFIER silent_mutation Average:63.995; most accessible tissue: Callus, score: 83.362 N N N N
vg0315006256 A -> G LOC_Os03g26210.1 downstream_gene_variant ; 4051.0bp to feature; MODIFIER silent_mutation Average:63.995; most accessible tissue: Callus, score: 83.362 N N N N
vg0315006256 A -> G LOC_Os03g26240.1 downstream_gene_variant ; 2499.0bp to feature; MODIFIER silent_mutation Average:63.995; most accessible tissue: Callus, score: 83.362 N N N N
vg0315006256 A -> G LOC_Os03g26210.3 downstream_gene_variant ; 4051.0bp to feature; MODIFIER silent_mutation Average:63.995; most accessible tissue: Callus, score: 83.362 N N N N
vg0315006256 A -> G LOC_Os03g26210.2 downstream_gene_variant ; 4051.0bp to feature; MODIFIER silent_mutation Average:63.995; most accessible tissue: Callus, score: 83.362 N N N N
vg0315006256 A -> G LOC_Os03g26229.1 intron_variant ; MODIFIER silent_mutation Average:63.995; most accessible tissue: Callus, score: 83.362 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315006256 9.05E-06 9.05E-06 mr1030 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
vg0315006256 2.81E-06 7.91E-10 mr1045 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
vg0315006256 3.27E-06 3.27E-06 mr1053 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
vg0315006256 3.89E-06 2.14E-07 mr1072 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
vg0315006256 NA 4.66E-06 mr1075 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
vg0315006256 NA 3.55E-06 mr1077 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
vg0315006256 NA 5.11E-06 mr1088 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
vg0315006256 NA 3.08E-07 mr1164 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
vg0315006256 4.58E-06 4.58E-06 mr1169 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
vg0315006256 NA 2.42E-06 mr1170 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
vg0315006256 NA 2.20E-06 mr1179 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
vg0315006256 NA 1.19E-06 mr1192 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
vg0315006256 NA 5.99E-07 mr1202 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
vg0315006256 NA 2.12E-06 mr1236 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
vg0315006256 NA 5.87E-06 mr1263 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
vg0315006256 NA 6.28E-08 mr1280 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
vg0315006256 NA 1.82E-07 mr1289 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
vg0315006256 NA 9.19E-06 mr1318 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
vg0315006256 NA 3.11E-07 mr1330 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
vg0315006256 NA 7.48E-07 mr1359 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
vg0315006256 NA 5.72E-06 mr1380 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
vg0315006256 6.41E-06 6.41E-06 mr1430 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
vg0315006256 NA 5.87E-06 mr1451 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
vg0315006256 NA 2.10E-08 mr1521 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
vg0315006256 4.42E-06 4.42E-06 mr1556 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
vg0315006256 NA 2.39E-06 mr1570 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
vg0315006256 NA 3.14E-07 mr1576 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
vg0315006256 NA 5.83E-06 mr1596 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
vg0315006256 NA 1.71E-06 mr1668 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
vg0315006256 NA 1.71E-06 mr1683 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
vg0315006256 NA 6.68E-07 mr1723 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
vg0315006256 NA 7.70E-11 mr1729 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
vg0315006256 NA 2.29E-06 mr1740 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
vg0315006256 NA 8.38E-07 mr1741 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
vg0315006256 NA 1.10E-07 mr1788 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
vg0315006256 NA 8.76E-06 mr1809 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
vg0315006256 NA 4.88E-08 mr1844 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
vg0315006256 NA 8.18E-06 mr1982 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