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Detailed information for vg0416328791:

Variant ID: vg0416328791 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16328791
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAGCAGTCCAAGAAACAGTCGTAAAGAACCAGTCAAGTTGCTCCAAGAGAGGTGAATTCTGCATATTACTCCACGTGTAAGACCTACCTTTCAAAGGCA[A/G]
CTCAAGGAGACCAAGATTACTGATTATATTATTGAAAATCATCATGTCATTCATATCCCAACCTGCCCTATTTTTGTTCTCAACAGATCTGTAAAAGTTA

Reverse complement sequence

TAACTTTTACAGATCTGTTGAGAACAAAAATAGGGCAGGTTGGGATATGAATGACATGATGATTTTCAATAATATAATCAGTAATCTTGGTCTCCTTGAG[T/C]
TGCCTTTGAAAGGTAGGTCTTACACGTGGAGTAATATGCAGAATTCACCTCTCTTGGAGCAACTTGACTGGTTCTTTACGACTGTTTCTTGGACTGCTTC

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	73.20%	14.40%	8.84%	3.51%	NA
All Indica	2759	82.20%	6.60%	11.20%	0.00%	NA
All Japonica	1512	63.90%	21.80%	3.44%	10.91%	NA
Aus	269	48.70%	46.50%	4.83%	0.00%	NA
Indica I	595	90.90%	1.80%	7.23%	0.00%	NA
Indica II	465	93.30%	2.80%	3.87%	0.00%	NA
Indica III	913	67.50%	11.80%	20.70%	0.00%	NA
Indica Intermediate	786	86.10%	6.40%	7.51%	0.00%	NA
Temperate Japonica	767	69.80%	8.30%	2.61%	19.30%	NA
Tropical Japonica	504	47.20%	46.00%	5.36%	1.39%	NA
Japonica Intermediate	241	80.10%	13.70%	2.07%	4.15%	NA
VI/Aromatic	96	24.00%	36.50%	39.58%	0.00%	NA
Intermediate	90	80.00%	12.20%	6.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0416328791	A -> DEL	LOC_Os04g27610.1	N	frameshift_variant	Average:18.72; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0416328791	A -> G	LOC_Os04g27610.1	synonymous_variant ; p.Leu95Leu; LOW	synonymous_codon	Average:18.72; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416328791	6.04E-07	NA	mr1011_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