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Detailed information for vg0431913843:

Variant ID: vg0431913843 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31913843
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAGTTGAAAGTTTTCAAATCCGACTTGAACGTTTTCAAATCGAGTTGAAAGTTTTTAAATCCGAGTTGAAAGTTTTCAAGTTTGAATTGAAAGTTTTC[A/G]
AATCTGAGTTGAAAGTTTTTAAATTTTTACTTAAAAGTTTCCAAATCTGAGTTAAAAGTTTCTAAATCTTGAATTGAATTTTTTCAAATATTGACTCCTA

Reverse complement sequence

TAGGAGTCAATATTTGAAAAAATTCAATTCAAGATTTAGAAACTTTTAACTCAGATTTGGAAACTTTTAAGTAAAAATTTAAAAACTTTCAACTCAGATT[T/C]
GAAAACTTTCAATTCAAACTTGAAAACTTTCAACTCGGATTTAAAAACTTTCAACTCGATTTGAAAACGTTCAAGTCGGATTTGAAAACTTTCAACTCGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.60%	1.00%	2.48%	0.00%	NA
All Indica	2759	99.60%	0.00%	0.43%	0.00%	NA
All Japonica	1512	90.40%	2.90%	6.68%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.50%	0.00%	1.51%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	82.10%	5.30%	12.52%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	97.90%	0.40%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	2.20%	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
vg0431913843	A -> G	LOC_Os04g53544.1	upstream_gene_variant ; 3276.0bp to feature; MODIFIER	silent_mutation	Average:16.341; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0431913843	A -> G	LOC_Os04g53544-LOC_Os04g53550	intergenic_region ; MODIFIER	silent_mutation	Average:16.341; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431913843	6.90E-06	NA	mr1310_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
vg0431913843	4.91E-06	NA	mr1959_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