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Detailed information for vg0331907206:

Variant ID: vg0331907206 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 31907206
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATAACTTATAATCTAAAACAGATTGAGTAATATTCAGAGGTGAATGCTACTCCTGACATAATAGGAGTACTTACTCCGTCTCAAAATGTAGCTATGTT[A/G]
TATAGGATGTGTTATTACCTAGTACTACAAATCTGGATAAGAGGTAGTATATATCTCTCCTGACATAATAGGAGTACTCCATTCATCCCAAAAAAACTCA

Reverse complement sequence

TGAGTTTTTTTGGGATGAATGGAGTACTCCTATTATGTCAGGAGAGATATATACTACCTCTTATCCAGATTTGTAGTACTAGGTAATAACACATCCTATA[T/C]
AACATAGCTACATTTTGAGACGGAGTAAGTACTCCTATTATGTCAGGAGTAGCATTCACCTCTGAATATTACTCAATCTGTTTTAGATTATAAGTTATTT

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%	7.60%	1.93%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	71.30%	22.80%	5.95%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	52.90%	37.20%	9.91%	0.00%	NA
Tropical Japonica	504	95.60%	3.60%	0.79%	0.00%	NA
Japonica Intermediate	241	78.80%	17.00%	4.15%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	11.10%	1.11%	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
vg0331907206	A -> G	LOC_Os03g56040.1	upstream_gene_variant ; 3524.0bp to feature; MODIFIER	silent_mutation	Average:46.152; most accessible tissue: Callus, score: 92.342	N	N	N	N
vg0331907206	A -> G	LOC_Os03g56030-LOC_Os03g56040	intergenic_region ; MODIFIER	silent_mutation	Average:46.152; most accessible tissue: Callus, score: 92.342	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0331907206	NA	2.47E-16	Heading_date	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0331907206	NA	1.61E-14	Heading_date	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0331907206	1.68E-07	NA	mr1354	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
vg0331907206	NA	1.25E-10	mr1354	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
vg0331907206	4.54E-06	2.05E-08	mr1829	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
vg0331907206	NA	9.82E-07	mr1829	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
vg0331907206	NA	5.01E-09	mr1002_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
vg0331907206	NA	4.79E-06	mr1138_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
vg0331907206	2.50E-08	NA	mr1354_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
vg0331907206	NA	1.17E-11	mr1354_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
vg0331907206	NA	9.71E-06	mr1549_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
vg0331907206	3.23E-06	4.95E-10	mr1829_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
vg0331907206	NA	3.28E-07	mr1829_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
vg0331907206	1.23E-06	5.05E-15	mr1902_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
vg0331907206	NA	1.26E-08	mr1902_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