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Detailed information for vg0501987126:

Variant ID: vg0501987126 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 1987126
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCAACAATATGTCCATCTTTGCCCCAAAAAAGAACAAGTATATTTTTCACGATGATTAGACACATTGGTAGCACTAGTAGATTTAGCAACATGAGCAAC[A/T]
ACAGGAGATTTTGCATGCACAACATTGGATTTTGAAGAAGATGCATTCATAGTAGATATGATACCAGCAGATTTAAACACAGTTTTATTAGTATCAGGTT

Reverse complement sequence

AACCTGATACTAATAAAACTGTGTTTAAATCTGCTGGTATCATATCTACTATGAATGCATCTTCTTCAAAATCCAATGTTGTGCATGCAAAATCTCCTGT[T/A]
GTTGCTCATGTTGCTAAATCTACTAGTGCTACCAATGTGTCTAATCATCGTGAAAAATATACTTGTTCTTTTTTGGGGCAAAGATGGACATATTGTTGGT

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	86.40%	11.50%	2.07%	0.00%	NA
All Indica	2759	78.10%	18.70%	3.19%	0.00%	NA
All Japonica	1512	99.60%	0.30%	0.07%	0.00%	NA
Aus	269	90.70%	5.90%	3.35%	0.00%	NA
Indica I	595	72.10%	23.40%	4.54%	0.00%	NA
Indica II	465	94.20%	5.60%	0.22%	0.00%	NA
Indica III	913	70.60%	24.90%	4.49%	0.00%	NA
Indica Intermediate	786	81.70%	15.90%	2.42%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0501987126	A -> T	LOC_Os05g04350.1	synonymous_variant ; p.Val329Val; LOW	synonymous_codon	Average:20.849; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0501987126	NA	7.89E-06	mr1265	Ind_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
vg0501987126	7.40E-08	9.74E-09	mr1332	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