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Detailed information for vg0406334961:

Variant ID: vg0406334961 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6334961
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGGCTCTTTATTGGACACAAAAAGAAAAACAAAGACACGAGTGAAGCAAAAATGACTCACTTGGTTGGAAGACCAAGGAGCCAACTTTATTTTATTTT[T/A]
TTATTCTCTTTTTTTATTTTATCTCTTTATGGCAACAATGGATATGGTGGGTATCCTGGCAGGATGGACACATGAGATGAGGATGCACATGGTGTATGAG

Reverse complement sequence

CTCATACACCATGTGCATCCTCATCTCATGTGTCCATCCTGCCAGGATACCCACCATATCCATTGTTGCCATAAAGAGATAAAATAAAAAAAGAGAATAA[A/T]
AAAATAAAATAAAGTTGGCTCCTTGGTCTTCCAACCAAGTGAGTCATTTTTGCTTCACTCGTGTCTTTGTTTTTCTTTTTGTGTCCAATAAAGAGCCAAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.10%	1.80%	6.03%	25.10%	NA
All Indica	2759	50.60%	2.90%	9.97%	36.50%	NA
All Japonica	1512	97.90%	0.10%	0.00%	1.92%	NA
Aus	269	48.00%	1.10%	2.97%	47.96%	NA
Indica I	595	29.70%	5.00%	10.92%	54.29%	NA
Indica II	465	33.50%	1.30%	5.59%	59.57%	NA
Indica III	913	68.60%	3.10%	11.17%	17.20%	NA
Indica Intermediate	786	55.60%	2.20%	10.43%	31.81%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	95.60%	0.20%	0.00%	4.17%	NA
Japonica Intermediate	241	96.70%	0.40%	0.00%	2.90%	NA
VI/Aromatic	96	94.80%	0.00%	2.08%	3.12%	NA
Intermediate	90	80.00%	0.00%	0.00%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406334961	T -> DEL	N	N	silent_mutation	Average:37.271; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0406334961	T -> A	LOC_Os04g11560.1	downstream_gene_variant ; 2266.0bp to feature; MODIFIER	silent_mutation	Average:37.271; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0406334961	T -> A	LOC_Os04g11550-LOC_Os04g11560	intergenic_region ; MODIFIER	silent_mutation	Average:37.271; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406334961	1.24E-07	1.24E-07	mr1300	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