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Detailed information for vg1020420315:

Variant ID: vg1020420315 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 20420315
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGGTCATGATTACCATCAAACACTTATCAAAGCTAAAAAAAACTATTCTAACAAAAAAAATTTAAAAGTAAGAGTGATCTTTTTTTTAAAAAAAGAGAG[C/A]
GAAATGATTTTAAATACATTAGAGTAAGGAAAATCAGGGGCCCGGTTCGGCTGACCACTTGCACACCCTCATGGAGGACCATGTTTGAACTTGAAGCATG

Reverse complement sequence

CATGCTTCAAGTTCAAACATGGTCCTCCATGAGGGTGTGCAAGTGGTCAGCCGAACCGGGCCCCTGATTTTCCTTACTCTAATGTATTTAAAATCATTTC[G/T]
CTCTCTTTTTTTAAAAAAAAGATCACTCTTACTTTTAAATTTTTTTTGTTAGAATAGTTTTTTTTAGCTTTGATAAGTGTTTGATGGTAATCATGACCAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.50% 37.40% 0.13% 0.00% NA
All Indica  2759 98.00% 1.80% 0.22% 0.00% NA
All Japonica  1512 7.90% 92.10% 0.00% 0.00% NA
Aus  269 27.90% 72.10% 0.00% 0.00% NA
Indica I  595 98.00% 1.70% 0.34% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 98.80% 1.10% 0.11% 0.00% NA
Indica Intermediate  786 96.60% 3.10% 0.38% 0.00% NA
Temperate Japonica  767 2.20% 97.80% 0.00% 0.00% NA
Tropical Japonica  504 18.50% 81.50% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 55.60% 44.40% 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
vg1020420315 C -> A LOC_Os10g38110.1 upstream_gene_variant ; 3824.0bp to feature; MODIFIER silent_mutation Average:47.017; most accessible tissue: Callus, score: 74.022 N N N N
vg1020420315 C -> A LOC_Os10g38110-LOC_Os10g38120 intergenic_region ; MODIFIER silent_mutation Average:47.017; most accessible tissue: Callus, score: 74.022 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1020420315 2.24E-09 1.49E-53 mr1509 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
vg1020420315 NA 4.77E-07 mr1509 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
vg1020420315 1.09E-11 1.83E-61 mr1558 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
vg1020420315 NA 2.73E-08 mr1558 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
vg1020420315 NA 2.99E-06 mr1990 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
vg1020420315 9.90E-16 2.81E-66 mr1509_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
vg1020420315 1.25E-07 5.83E-11 mr1509_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
vg1020420315 NA 1.90E-13 mr1514_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
vg1020420315 7.21E-22 1.13E-86 mr1558_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
vg1020420315 2.71E-11 1.80E-17 mr1558_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