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Detailed information for vg0707146260:

Variant ID: vg0707146260 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7146260
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

AATCTAATGCGAACTTCCCCTTGTCTTGGGGTGCTTGAATCACCTACTGAGATTGTGGATATGCTCTTTTCGATTCAACTGCAAGTATTTGTTTTTAATC[A/T]
TGTGATGTGAACAACACTAATGTTTAAATTTTCGAAGGCATAACATGACACTTGGTTTAGGTGTAACTGTCTTACAAATATATGCTCTTTTTTTTGTTTG

Reverse complement sequence

CAAACAAAAAAAAGAGCATATATTTGTAAGACAGTTACACCTAAACCAAGTGTCATGTTATGCCTTCGAAAATTTAAACATTAGTGTTGTTCACATCACA[T/A]
GATTAAAAACAAATACTTGCAGTTGAATCGAAAAGAGCATATCCACAATCTCAGTAGGTGATTCAAGCACCCCAAGACAAGGGGAAGTTCGCATTAGATT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.50%	1.90%	1.61%	0.00%	NA
All Indica	2759	94.20%	3.20%	2.61%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	90.80%	4.20%	5.04%	0.00%	NA
Indica II	465	95.90%	0.00%	4.09%	0.00%	NA
Indica III	913	95.60%	4.10%	0.33%	0.00%	NA
Indica Intermediate	786	94.10%	3.30%	2.54%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	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
vg0707146260	A -> T	LOC_Os07g12520.1	intron_variant ; MODIFIER	silent_mutation	Average:68.216; most accessible tissue: Minghui63 flag leaf, score: 85.5	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707146260	3.92E-06	3.92E-06	mr1499	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