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Detailed information for vg0403070551:

Variant ID: vg0403070551 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3070551
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGTTCCTGAAAAACAGCTTCAGCCTTGGTATTATAGGAAAATACCACATCACCTTAGCAGGAATTCTCTTCTTCAAAGGCTGTCCGTCAACTTCACCT[G/A]
GATCATCTCATCTTATCTTGTATCGTAGTGCTTTGCAAACAGGGCATGCTTCCAGGTTTTCGTACTCACCGCAATACAGCATACAGTCATTCGGACACGC

Reverse complement sequence

GCGTGTCCGAATGACTGTATGCTGTATTGCGGTGAGTACGAAAACCTGGAAGCATGCCCTGTTTGCAAAGCACTACGATACAAGATAAGATGAGATGATC[C/T]
AGGTGAAGTTGACGGACAGCCTTTGAAGAAGAGAATTCCTGCTAAGGTGATGTGGTATTTTCCTATAATACCAAGGCTGAAGCTGTTTTTCAGGAACAAA

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	74.20%	1.30%	1.86%	22.62%	NA
All Indica	2759	78.70%	2.10%	2.36%	16.82%	NA
All Japonica	1512	66.10%	0.10%	0.53%	33.33%	NA
Aus	269	79.20%	0.00%	4.09%	16.73%	NA
Indica I	595	97.00%	0.00%	0.17%	2.86%	NA
Indica II	465	76.80%	1.30%	1.29%	20.65%	NA
Indica III	913	67.00%	5.50%	4.49%	23.00%	NA
Indica Intermediate	786	79.50%	0.40%	2.16%	17.94%	NA
Temperate Japonica	767	86.80%	0.00%	0.26%	12.91%	NA
Tropical Japonica	504	38.50%	0.00%	0.79%	60.71%	NA
Japonica Intermediate	241	57.70%	0.40%	0.83%	41.08%	NA
VI/Aromatic	96	51.00%	1.00%	3.12%	44.79%	NA
Intermediate	90	83.30%	1.10%	1.11%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403070551	G -> DEL	N	N	silent_mutation	Average:8.246; most accessible tissue: Callus, score: 24.662	N	N	N	N
vg0403070551	G -> A	LOC_Os04g05920.1	upstream_gene_variant ; 4159.0bp to feature; MODIFIER	silent_mutation	Average:8.246; most accessible tissue: Callus, score: 24.662	N	N	N	N
vg0403070551	G -> A	LOC_Os04g05930.1	upstream_gene_variant ; 851.0bp to feature; MODIFIER	silent_mutation	Average:8.246; most accessible tissue: Callus, score: 24.662	N	N	N	N
vg0403070551	G -> A	LOC_Os04g05940.1	intron_variant ; MODIFIER	silent_mutation	Average:8.246; most accessible tissue: Callus, score: 24.662	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403070551	3.18E-07	NA	mr1695_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
vg0403070551	3.88E-06	2.95E-09	mr1695_2	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