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Detailed information for vg0334068822:

Variant ID: vg0334068822 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34068822
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAAGCATAATTAATTCGTCATTAGCAAATGTTTAATGTAGCACCACATTATCAGATCATGGCGCAATTAGGCTTAAAAGATTTATCTCGCAATTTACAT[A/G]
TAAACTGTGTAATTAGTTTTTTGTTTGTTAATATTTAATACTCCAGTCCATACATATGTATTCAAATGTTGAATGTGATGGGGGCAAAAAAGAAAATTGC

Reverse complement sequence

GCAATTTTCTTTTTTGCCCCCATCACATTCAACATTTGAATACATATGTATGGACTGGAGTATTAAATATTAACAAACAAAAAACTAATTACACAGTTTA[T/C]
ATGTAAATTGCGAGATAAATCTTTTAAGCCTAATTGCGCCATGATCTGATAATGTGGTGCTACATTAAACATTTGCTAATGACGAATTAATTATGCTTAA

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	62.30%	1.70%	2.43%	33.62%	NA
All Indica	2759	47.30%	2.10%	3.37%	47.26%	NA
All Japonica	1512	99.40%	0.10%	0.07%	0.46%	NA
Aus	269	5.90%	5.60%	2.23%	86.25%	NA
Indica I	595	68.20%	0.70%	6.72%	24.37%	NA
Indica II	465	21.70%	3.40%	2.58%	72.26%	NA
Indica III	913	50.30%	2.20%	2.30%	45.24%	NA
Indica Intermediate	786	43.00%	2.30%	2.54%	52.16%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	98.80%	0.20%	0.00%	0.99%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	68.80%	1.00%	12.50%	17.71%	NA
Intermediate	90	60.00%	4.40%	3.33%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334068822	A -> DEL	N	N	silent_mutation	Average:39.327; most accessible tissue: Callus, score: 70.017	N	N	N	N
vg0334068822	A -> G	LOC_Os03g59830.1	upstream_gene_variant ; 293.0bp to feature; MODIFIER	silent_mutation	Average:39.327; most accessible tissue: Callus, score: 70.017	N	N	N	N
vg0334068822	A -> G	LOC_Os03g59840.1	downstream_gene_variant ; 1600.0bp to feature; MODIFIER	silent_mutation	Average:39.327; most accessible tissue: Callus, score: 70.017	N	N	N	N
vg0334068822	A -> G	LOC_Os03g59820-LOC_Os03g59830	intergenic_region ; MODIFIER	silent_mutation	Average:39.327; most accessible tissue: Callus, score: 70.017	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334068822	4.12E-06	NA	mr1874_2	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