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Detailed information for vg0417444653:

Variant ID: vg0417444653 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17444653
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCGGAGTTAGGATAAGGATGGGTGGGTGGGTCTCATGTGTGTGGATGGATAAGGACAGGTGCCCCGCCGAGTCGGCTAGGTTTTATGGGTGCTCGTTCT[A/G]
CAAAATGGGTACTAATAGTGTTGGAACGAGATTTTCACTATAACCAACACTACTATTGCTGAAATGTGCCAGTTTAATTAACATTTTTCCATCTCGCGGA

Reverse complement sequence

TCCGCGAGATGGAAAAATGTTAATTAAACTGGCACATTTCAGCAATAGTAGTGTTGGTTATAGTGAAAATCTCGTTCCAACACTATTAGTACCCATTTTG[T/C]
AGAACGAGCACCCATAAAACCTAGCCGACTCGGCGGGGCACCTGTCCTTATCCATCCACACACATGAGACCCACCCACCCATCCTTATCCTAACTCCGCC

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	83.90%	15.30%	0.08%	0.70%	NA
All Indica	2759	92.50%	6.20%	0.04%	1.20%	NA
All Japonica	1512	75.10%	24.80%	0.13%	0.00%	NA
Aus	269	52.00%	47.60%	0.37%	0.00%	NA
Indica I	595	79.50%	20.30%	0.17%	0.00%	NA
Indica II	465	99.10%	0.60%	0.00%	0.22%	NA
Indica III	913	95.70%	2.10%	0.00%	2.19%	NA
Indica Intermediate	786	94.80%	3.70%	0.00%	1.53%	NA
Temperate Japonica	767	58.00%	41.90%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	78.40%	21.20%	0.41%	0.00%	NA
VI/Aromatic	96	61.50%	38.50%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0417444653	A -> DEL	N	N	silent_mutation	Average:55.774; most accessible tissue: Zhenshan97 young leaf, score: 89.666	N	N	N	N
vg0417444653	A -> G	LOC_Os04g29360.1	downstream_gene_variant ; 2178.0bp to feature; MODIFIER	silent_mutation	Average:55.774; most accessible tissue: Zhenshan97 young leaf, score: 89.666	N	N	N	N
vg0417444653	A -> G	LOC_Os04g29350-LOC_Os04g29360	intergenic_region ; MODIFIER	silent_mutation	Average:55.774; most accessible tissue: Zhenshan97 young leaf, score: 89.666	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417444653	6.07E-06	NA	mr1549_2	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
vg0417444653	NA	4.79E-07	mr1807_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