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Detailed information for vg0708138138:

Variant ID: vg0708138138 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8138138
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

TGTATTGCTAATGTCGCCTGTTAAAATTTTGTCTGTACTACTATTTAAGGAAATCTCCGGGCAGATAATGAATTTGCGTGATCATTTGCTGGTTCTGCAC[A/G]
TGATGCACTGAACATGGAGTTCTGTGTTATCTAAATGTATTCTATTGTGTGCACAGATGGATGGGAAAGTCGGTGGGTCAAGTCAGAATGGAAGAAGGAT

Reverse complement sequence

ATCCTTCTTCCATTCTGACTTGACCCACCGACTTTCCCATCCATCTGTGCACACAATAGAATACATTTAGATAACACAGAACTCCATGTTCAGTGCATCA[T/C]
GTGCAGAACCAGCAAATGATCACGCAAATTCATTATCTGCCCGGAGATTTCCTTAAATAGTAGTACAGACAAAATTTTAACAGGCGACATTAGCAATACA

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	98.90%	0.80%	0.28%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	96.50%	2.60%	0.86%	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	93.10%	5.20%	1.69%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	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
vg0708138138	A -> G	LOC_Os07g14270.1	intron_variant ; MODIFIER	silent_mutation	Average:67.49; most accessible tissue: Minghui63 flower, score: 79.507	N	N	N	N
vg0708138138	A -> G	LOC_Os07g14270.2	intron_variant ; MODIFIER	silent_mutation	Average:67.49; most accessible tissue: Minghui63 flower, score: 79.507	N	N	N	N
vg0708138138	A -> G	LOC_Os07g14270.3	intron_variant ; MODIFIER	silent_mutation	Average:67.49; most accessible tissue: Minghui63 flower, score: 79.507	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708138138	1.14E-06	1.14E-06	mr1004_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
vg0708138138	NA	7.27E-06	mr1161_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251