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Detailed information for vg0228609636:

Variant ID: vg0228609636 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28609636
Reference Allele: G	Alternative Allele: A,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCTCACTATTGTTCCCTTCTTGTGATCGCTACGTGAGTAAGGGGTGTCTTCATTTGATAGGAGGATGCTAGGGTCAATCATCACCGTGAAAGGGGGTT[G/A,C]
CCCATCAAACTGATCATAATCCTCGTCAGTCTTGTCCTCAACTCCGACGATTTTCTTTTGCCTGAGAGAACCACATGACGCTTTGGCTCGTCAGGCCCTC

Reverse complement sequence

GAGGGCCTGACGAGCCAAAGCGTCATGTGGTTCTCTCAGGCAAAAGAAAATCGTCGGAGTTGAGGACAAGACTGACGAGGATTATGATCAGTTTGATGGG[C/T,G]
AACCCCCTTTCACGGTGATGATTGACCCTAGCATCCTCCTATCAAATGAAGACACCCCTTACTCACGTAGCGATCACAAGAAGGGAACAATAGTGAGGAG

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	94.30%	4.70%	0.91%	0.00%	C: 0.02%
All Indica	2759	99.60%	0.30%	0.04%	0.00%	C: 0.04%
All Japonica	1512	83.40%	13.90%	2.71%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.00%	C: 0.22%
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.80%	0.13%	0.00%	NA
Temperate Japonica	767	70.80%	23.90%	5.35%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	90.00%	10.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg0228609636	G -> A	LOC_Os02g46900.1	synonymous_variant ; p.Gly732Gly; LOW	synonymous_codon	Average:17.877; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0228609636	G -> C	LOC_Os02g46900.1	synonymous_variant ; p.Gly732Gly; LOW	synonymous_codon	Average:17.877; 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
vg0228609636	4.88E-06	NA	mr1100	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