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Detailed information for vg0625671188:

Variant ID: vg0625671188 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 25671188
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTTAAGTACATGTATTATGCCATCAAGAATGGTGCTACTGTTCCAGGTGTCACAGATTCAGATTAGAGTGTTTTCCCATGCTATTGCCCTCCAGCAATT[A/G]
CACAAGCTGAAAATAAACAAGAACGCCACGCCATTTCAGAACACGATGCTCCTGTTTCATTTTAGTATCTTATAGCCCAAATGTACATATATATAATACA

Reverse complement sequence

TGTATTATATATATGTACATTTGGGCTATAAGATACTAAAATGAAACAGGAGCATCGTGTTCTGAAATGGCGTGGCGTTCTTGTTTATTTTCAGCTTGTG[T/C]
AATTGCTGGAGGGCAATAGCATGGGAAAACACTCTAATCTGAATCTGTGACACCTGGAACAGTAGCACCATTCTTGATGGCATAATACATGTACTTAACC

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	97.80%	2.20%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.20%	6.80%	0.00%	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	100.00%	0.00%	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	87.60%	12.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0625671188	A -> G	LOC_Os06g42680.1	intron_variant ; MODIFIER	silent_mutation	Average:60.831; most accessible tissue: Callus, score: 85.775	N	N	N	N
vg0625671188	A -> G	LOC_Os06g42680.2	intron_variant ; MODIFIER	silent_mutation	Average:60.831; most accessible tissue: Callus, score: 85.775	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0625671188	7.69E-07	7.69E-07	mr1036_2	Jap_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