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Detailed information for vg0401652221:

Variant ID: vg0401652221 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1652221
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTCCTGAGCAACCCATTCGGTGTAGTCAGGATTGGGAACAACAATGTCCTTCTCATCCTTTTTCACGATCTTGGTTGGAGCCGGCATCTCCTTGGTGCC[G/A]
TCAACGAACCCAGCCATCTGGGCCCCTCGCAGAGTCGCAAGGACCTGAGCTCGCCACAGGGAGAAGTTGCCGCGAGCCAGCTTCTCCGTCACCGGCTGCG

Reverse complement sequence

CGCAGCCGGTGACGGAGAAGCTGGCTCGCGGCAACTTCTCCCTGTGGCGAGCTCAGGTCCTTGCGACTCTGCGAGGGGCCCAGATGGCTGGGTTCGTTGA[C/T]
GGCACCAAGGAGATGCCGGCTCCAACCAAGATCGTGAAAAAGGATGAGAAGGACATTGTTGTTCCCAATCCTGACTACACCGAATGGGTTGCTCAGGAAC

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	67.10%	0.40%	2.26%	30.24%	NA
All Indica	2759	64.10%	0.70%	2.94%	32.29%	NA
All Japonica	1512	73.90%	0.00%	1.06%	25.07%	NA
Aus	269	59.10%	0.40%	2.60%	37.92%	NA
Indica I	595	78.80%	0.50%	2.02%	18.66%	NA
Indica II	465	71.00%	0.90%	1.94%	26.24%	NA
Indica III	913	46.90%	1.10%	4.71%	47.32%	NA
Indica Intermediate	786	68.80%	0.30%	2.16%	28.75%	NA
Temperate Japonica	767	88.70%	0.00%	1.04%	10.30%	NA
Tropical Japonica	504	53.00%	0.00%	0.99%	46.03%	NA
Japonica Intermediate	241	70.50%	0.00%	1.24%	28.22%	NA
VI/Aromatic	96	55.20%	0.00%	2.08%	42.71%	NA
Intermediate	90	81.10%	0.00%	1.11%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401652221	G -> DEL	LOC_Os04g03730.1	N	frameshift_variant	Average:22.725; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0401652221	G -> A	LOC_Os04g03730.1	synonymous_variant ; p.Asp48Asp; LOW	synonymous_codon	Average:22.725; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401652221	3.45E-06	3.45E-06	mr1398	Ind_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
vg0401652221	2.52E-06	2.52E-06	mr1714	Ind_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