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Detailed information for vg1203657863:

Variant ID: vg1203657863 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 3657863
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTACATCATATCTTTGGCTTCCTCTTACTTGTGTCCATTCCCTTTCTTGTTTATAGGATGCCACCTCGCAAGTCCATCTCGCGCAGGGGCAAGCGCCTCC[A/G]
GGATCGTTCCCCCACTCCTTCCCCATCCTCCTCGGAGGGCTCGGACAGTGAATGGTCTGGGGAAGGGTACGCGGGGACCGGTCCCCAAGTGACGCAAGTA

Reverse complement sequence

TACTTGCGTCACTTGGGGACCGGTCCCCGCGTACCCTTCCCCAGACCATTCACTGTCCGAGCCCTCCGAGGAGGATGGGGAAGGAGTGGGGGAACGATCC[T/C]
GGAGGCGCTTGCCCCTGCGCGAGATGGACTTGCGAGGTGGCATCCTATAAACAAGAAAGGGAATGGACACAAGTAAGAGGAAGCCAAAGATATGATGTAC

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 93.70% 6.30% 0.04% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 81.70% 18.20% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 67.00% 32.90% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 91.70% 8.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 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
vg1203657863 A -> G LOC_Os12g07410.1 upstream_gene_variant ; 411.0bp to feature; MODIFIER silent_mutation Average:61.27; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg1203657863 A -> G LOC_Os12g07420.1 upstream_gene_variant ; 4268.0bp to feature; MODIFIER silent_mutation Average:61.27; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg1203657863 A -> G LOC_Os12g07400-LOC_Os12g07410 intergenic_region ; MODIFIER silent_mutation Average:61.27; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1203657863 NA 1.96E-09 mr1002 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
vg1203657863 NA 7.32E-07 mr1002 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
vg1203657863 NA 8.15E-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
vg1203657863 NA 8.77E-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
vg1203657863 NA 3.11E-06 mr1271 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
vg1203657863 NA 7.60E-08 mr1271 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
vg1203657863 NA 2.33E-10 mr1282 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
vg1203657863 NA 2.09E-09 mr1658 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
vg1203657863 NA 4.64E-06 mr1977 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
vg1203657863 3.74E-07 1.81E-15 mr1002_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
vg1203657863 NA 3.37E-10 mr1002_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
vg1203657863 1.25E-06 1.63E-16 mr1182_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
vg1203657863 NA 4.93E-09 mr1182_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
vg1203657863 2.14E-06 1.70E-13 mr1282_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
vg1203657863 NA 6.68E-08 mr1282_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
vg1203657863 NA 1.36E-07 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