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Detailed information for vg0600002758:

Variant ID: vg0600002758 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 2758
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCATGAAACTGATGGGATCCTGATCCGTTGAAATTGTCCCTCATGCTGACCAATTGCTGCGGGCACAAGAGAGGGAGGGGGAGATGAGAGGGGTTACTA[A/G]
AGATGAGGTACTAAACCACTTGCCTATTGATCTGTGGTGAATGGATTTTATGATTCAAGTTGTTTAAGCAAACAACCTAGTATGGTCGCATCCCCACCAA

Reverse complement sequence

TTGGTGGGGATGCGACCATACTAGGTTGTTTGCTTAAACAACTTGAATCATAAAATCCATTCACCACAGATCAATAGGCAAGTGGTTTAGTACCTCATCT[T/C]
TAGTAACCCCTCTCATCTCCCCCTCCCTCTCTTGTGCCCGCAGCAATTGGTCAGCATGAGGGACAATTTCAACGGATCAGGATCCCATCAGTTTCATGGA

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	75.90%	3.10%	6.50%	14.56%	NA
All Indica	2759	62.60%	4.70%	8.81%	23.89%	NA
All Japonica	1512	99.80%	0.00%	0.07%	0.13%	NA
Aus	269	68.40%	5.20%	19.70%	6.69%	NA
Indica I	595	65.40%	6.90%	7.90%	19.83%	NA
Indica II	465	64.70%	0.60%	6.02%	28.60%	NA
Indica III	913	58.90%	3.30%	10.84%	26.94%	NA
Indica Intermediate	786	63.50%	7.10%	8.78%	20.61%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	85.40%	1.00%	9.38%	4.17%	NA
Intermediate	90	92.20%	1.10%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0600002758	A -> G	LOC_Os06g01010.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0600002758	A -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0600002758	1.16E-06	NA	mr1011	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