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Detailed information for vg0406137915:

Variant ID: vg0406137915 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6137915
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCTCGTTGCGTGAAGCCTTTTGCCACAAGTCGCGCCTTAAACTTTTCTATATTCCCTCTGGAGTCATATTTGGTTTTAAAGACCCATTTACAGCCTACT[G/A]
TTTTGGCTCCTTTTGGGAATTTCTTCTAAATCCCAGAAATCGTTTAGTTTCATTGATTTCATTTCATCTTTCATGGTTTCCAACCATTCAGATGAGCGTG

Reverse complement sequence

CACGCTCATCTGAATGGTTGGAAACCATGAAAGATGAAATGAAATCAATGAAACTAAACGATTTCTGGGATTTAGAAGAAATTCCCAAAAGGAGCCAAAA[C/T]
AGTAGGCTGTAAATGGGTCTTTAAAACCAAATATGACTCCAGAGGGAATATAGAAAAGTTTAAGGCGCGACTTGTGGCAAAAGGCTTCACGCAACGAGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.50%	2.70%	0.47%	6.35%	NA
All Indica	2759	87.00%	3.10%	0.47%	9.46%	NA
All Japonica	1512	94.80%	2.80%	0.53%	1.85%	NA
Aus	269	97.80%	0.00%	0.37%	1.86%	NA
Indica I	595	94.60%	0.00%	0.67%	4.71%	NA
Indica II	465	75.10%	15.50%	0.86%	8.60%	NA
Indica III	913	90.60%	0.20%	0.22%	8.98%	NA
Indica Intermediate	786	84.10%	1.40%	0.38%	14.12%	NA
Temperate Japonica	767	93.50%	5.50%	0.91%	0.13%	NA
Tropical Japonica	504	95.00%	0.00%	0.20%	4.76%	NA
Japonica Intermediate	241	98.30%	0.40%	0.00%	1.24%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	93.30%	1.10%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406137915	G -> DEL	N	N	silent_mutation	Average:14.955; most accessible tissue: Zhenshan97 flag leaf, score: 39.027	N	N	N	N
vg0406137915	G -> A	LOC_Os04g11240.1	upstream_gene_variant ; 3287.0bp to feature; MODIFIER	silent_mutation	Average:14.955; most accessible tissue: Zhenshan97 flag leaf, score: 39.027	N	N	N	N
vg0406137915	G -> A	LOC_Os04g11230.1	intron_variant ; MODIFIER	silent_mutation	Average:14.955; most accessible tissue: Zhenshan97 flag leaf, score: 39.027	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406137915	1.05E-06	3.06E-08	mr1549_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
vg0406137915	8.09E-06	2.67E-07	mr1757_2	Jap_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