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Detailed information for vg0127319721:

Variant ID: vg0127319721 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 27319721
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCTGTTTATTTGTATACTCTAATATCACATCTGTTAGTATCAGAACCATAAACTTGCAGATGCAAGCATAGATATCATGCCAACCACATGACTATCTCA[A/G]
TATTAGCCAGTTGAACCAGTTGAAATTTGTAGTCCTACAAACTAAACCTCCCTGATCAAATGAAGAAGTTCCACGGCTGAAGGGATTAGCCATGGGACTT

Reverse complement sequence

AAGTCCCATGGCTAATCCCTTCAGCCGTGGAACTTCTTCATTTGATCAGGGAGGTTTAGTTTGTAGGACTACAAATTTCAACTGGTTCAACTGGCTAATA[T/C]
TGAGATAGTCATGTGGTTGGCATGATATCTATGCTTGCATCTGCAAGTTTATGGTTCTGATACTAACAGATGTGATATTAGAGTATACAAATAAACAGGG

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	93.80%	5.80%	0.36%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	81.50%	17.40%	1.12%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	66.40%	31.70%	1.96%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	91.30%	7.90%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	0.00%	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
vg0127319721	A -> G	LOC_Os01g47750.1	intron_variant ; MODIFIER	silent_mutation	Average:69.268; most accessible tissue: Callus, score: 86.442	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0127319721	5.60E-07	NA	mr1648_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