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Detailed information for vg0420210561:

Variant ID: vg0420210561 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20210561
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAGACGTGGGGAGCCAACTAGTGGGTGCATGGATTATTCGTACCATGCTTTTTGAAGTGTAATATTTTCTAAGATATCTTTTTCTAATATATTTGTTA[G/A]
TTTATGATATTCAATTCATCCATATGAGTTATTTTTCTCTATCAATATTATCTATTCAATCATGCAGTTAGAAACACGTCTTTAGTCATGTAGCTACCTA

Reverse complement sequence

TAGGTAGCTACATGACTAAAGACGTGTTTCTAACTGCATGATTGAATAGATAATATTGATAGAGAAAAATAACTCATATGGATGAATTGAATATCATAAA[C/T]
TAACAAATATATTAGAAAAAGATATCTTAGAAAATATTACACTTCAAAAAGCATGGTACGAATAATCCATGCACCCACTAGTTGGCTCCCCACGTCTTTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.60%	4.80%	0.55%	0.00%	NA
All Indica	2759	99.20%	0.70%	0.14%	0.00%	NA
All Japonica	1512	85.40%	13.40%	1.19%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	96.80%	2.80%	0.43%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.60%	0.13%	0.00%	NA
Temperate Japonica	767	99.10%	0.10%	0.78%	0.00%	NA
Tropical Japonica	504	60.10%	37.90%	1.98%	0.00%	NA
Japonica Intermediate	241	94.60%	4.60%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	6.70%	3.33%	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
vg0420210561	G -> A	LOC_Os04g33370.1	upstream_gene_variant ; 779.0bp to feature; MODIFIER	silent_mutation	Average:44.461; most accessible tissue: Callus, score: 74.979	N	N	N	N
vg0420210561	G -> A	LOC_Os04g33380.1	downstream_gene_variant ; 4378.0bp to feature; MODIFIER	silent_mutation	Average:44.461; most accessible tissue: Callus, score: 74.979	N	N	N	N
vg0420210561	G -> A	LOC_Os04g33360-LOC_Os04g33370	intergenic_region ; MODIFIER	silent_mutation	Average:44.461; most accessible tissue: Callus, score: 74.979	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420210561	2.30E-06	3.91E-08	mr1925	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
vg0420210561	2.46E-08	8.52E-10	mr1498_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