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Detailed information for vg0719602226:

Variant ID: vg0719602226 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19602226
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGTGTTGTGATATACTACCTCCGTCCCAAAATGTAACAATTTAGAATTGGATGAGACGTATCCTGTATCTGAATAAAGGTCTCTCCAGATACGTTCTA[C/A]
TAGGTGTCCCATCTAAACATAGGTTGTTATATTTTAAGACGGATGGAGTAGCCTAAAAATGCGTATTATCGGATAGCCCTTTTATCATATATAATCCGTA

Reverse complement sequence

TACGGATTATATATGATAAAAGGGCTATCCGATAATACGCATTTTTAGGCTACTCCATCCGTCTTAAAATATAACAACCTATGTTTAGATGGGACACCTA[G/T]
TAGAACGTATCTGGAGAGACCTTTATTCAGATACAGGATACGTCTCATCCAATTCTAAATTGTTACATTTTGGGACGGAGGTAGTATATCACAACACCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.50% 1.50% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.30% 4.60% 0.13% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 90.90% 8.90% 0.26% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0719602226 C -> A LOC_Os07g32774.1 intron_variant ; MODIFIER silent_mutation Average:49.895; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg0719602226 C -> A LOC_Os07g32774.2 intron_variant ; MODIFIER silent_mutation Average:49.895; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719602226 7.95E-06 7.95E-06 mr1024 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
vg0719602226 1.33E-07 9.74E-06 mr1842_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