Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0113106767:

Variant ID: vg0113106767 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13106767
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTTATATAATGTAGGTATGACGGTTGGCGAAGGGGAAATGTCCGAAGTACCCCGCAACCGCCATCAGGGAGTGATCTGGAGCGTCCACGCCTAACCCTA[G/A]
GATCAACGGTGATCAGGGGGGTTCGGCCGAACTTGGGTTGGGCCCTCTTGGCCTGGCCTTCGGTCGGTGGATTCCCTGATCCTTCCTCTATCCATTTTTC

Reverse complement sequence

GAAAAATGGATAGAGGAAGGATCAGGGAATCCACCGACCGAAGGCCAGGCCAAGAGGGCCCAACCCAAGTTCGGCCGAACCCCCCTGATCACCGTTGATC[C/T]
TAGGGTTAGGCGTGGACGCTCCAGATCACTCCCTGATGGCGGTTGCGGGGTACTTCGGACATTTCCCCTTCGCCAACCGTCATACCTACATTATATAAAG

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 90.20% 3.40% 0.47% 5.95% NA
All Indica  2759 90.00% 0.00% 0.76% 9.24% NA
All Japonica  1512 87.90% 10.50% 0.07% 1.52% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.60% 0.00% 0.00% 8.40% NA
Indica II  465 91.80% 0.00% 0.00% 8.17% NA
Indica III  913 86.50% 0.00% 1.86% 11.61% NA
Indica Intermediate  786 91.70% 0.00% 0.51% 7.76% NA
Temperate Japonica  767 97.70% 1.20% 0.00% 1.17% NA
Tropical Japonica  504 68.70% 28.80% 0.20% 2.38% NA
Japonica Intermediate  241 97.10% 2.10% 0.00% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 3.30% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0113106767 G -> A LOC_Os01g23330.1 intron_variant ; MODIFIER silent_mutation Average:52.321; most accessible tissue: Minghui63 young leaf, score: 72.408 N N N N
vg0113106767 G -> DEL N N silent_mutation Average:52.321; most accessible tissue: Minghui63 young leaf, score: 72.408 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113106767 NA 6.79E-07 mr1076 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
vg0113106767 NA 5.18E-08 mr1082 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
vg0113106767 5.67E-06 7.20E-10 mr1083 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
vg0113106767 9.06E-06 9.06E-06 mr1204 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
vg0113106767 NA 2.04E-08 mr1226 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
vg0113106767 NA 3.60E-06 mr1408 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
vg0113106767 NA 8.09E-06 mr1411 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
vg0113106767 NA 4.84E-06 mr1560 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
vg0113106767 NA 2.67E-06 mr1878 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
vg0113106767 NA 6.03E-07 mr1949 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
vg0113106767 2.37E-08 2.37E-08 mr1076_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
vg0113106767 5.18E-06 1.84E-09 mr1082_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
vg0113106767 1.82E-06 1.22E-09 mr1083_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
vg0113106767 3.20E-06 1.35E-06 mr1103_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
vg0113106767 2.79E-06 8.28E-07 mr1104_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
vg0113106767 NA 6.73E-06 mr1107_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
vg0113106767 9.36E-06 6.63E-09 mr1226_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
vg0113106767 5.84E-07 5.84E-07 mr1264_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
vg0113106767 NA 7.57E-07 mr1408_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
vg0113106767 NA 4.95E-07 mr1498_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