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Detailed information for vg1221003277:

Variant ID: vg1221003277 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 21003277
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGCGGGTCGACTCGCCGGCTCAGCTTGGTTTTCTATAGGTGTCGGTTCTTTAATTAACTGGCACCTATAATATTTTATTGATATCAGTTCTTTTAAAA[G/A]
ACCAACACCTACTCCCTCCATCCAAAAAAAACTAACCTAGTACTAGGATGGGACAAAAACCAACACCTACTCCCTCTGTCCCAAAAAAAGCTAACCTAGT

Reverse complement sequence

ACTAGGTTAGCTTTTTTTGGGACAGAGGGAGTAGGTGTTGGTTTTTGTCCCATCCTAGTACTAGGTTAGTTTTTTTTGGATGGAGGGAGTAGGTGTTGGT[C/T]
TTTTAAAAGAACTGATATCAATAAAATATTATAGGTGCCAGTTAATTAAAGAACCGACACCTATAGAAAACCAAGCTGAGCCGGCGAGTCGACCCGCATG

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 41.90% 19.00% 0.15% 38.95% NA
All Indica  2759 49.30% 1.50% 0.14% 49.04% NA
All Japonica  1512 33.30% 54.50% 0.13% 12.10% NA
Aus  269 3.30% 3.00% 0.37% 93.31% NA
Indica I  595 79.00% 1.00% 0.00% 20.00% NA
Indica II  465 43.70% 3.90% 0.43% 52.04% NA
Indica III  913 35.70% 0.70% 0.11% 63.53% NA
Indica Intermediate  786 45.90% 1.50% 0.13% 52.42% NA
Temperate Japonica  767 6.90% 86.00% 0.26% 6.78% NA
Tropical Japonica  504 77.40% 6.50% 0.00% 16.07% NA
Japonica Intermediate  241 24.90% 54.40% 0.00% 20.75% NA
VI/Aromatic  96 68.80% 2.10% 0.00% 29.17% NA
Intermediate  90 44.40% 26.70% 0.00% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1221003277 G -> DEL N N silent_mutation Average:56.491; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N
vg1221003277 G -> A LOC_Os12g34630-LOC_Os12g34640 intergenic_region ; MODIFIER silent_mutation Average:56.491; most accessible tissue: Zhenshan97 young leaf, score: 73.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1221003277 8.06E-06 NA mr1057 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
vg1221003277 NA 3.31E-06 mr1039_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
vg1221003277 2.88E-08 2.16E-07 mr1057_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
vg1221003277 NA 2.55E-08 mr1057_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
vg1221003277 NA 2.42E-07 mr1227_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
vg1221003277 NA 1.34E-06 mr1268_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
vg1221003277 NA 1.34E-06 mr1272_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
vg1221003277 NA 4.81E-08 mr1376_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
vg1221003277 NA 3.21E-08 mr1431_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
vg1221003277 NA 1.31E-09 mr1942_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