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Detailed information for vg1207888547:

Variant ID: vg1207888547 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7888547
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, T: 0.23, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

TAAATCGCGAGACGAATCTTTTGAGCCTAATTAGGCCATGATTAGCCATAAGTGCTACAGTAACCCACATGTGCTAATGCCAGCTTAAGTAGGCTCAAAA[T/G]
ATTCGTCTCGCGGTTTCCAGGCGAGTTCTGAAATTAGTTTTTTCATTCGTGTCCGAAAACCCCTTCCGACATTCGGTCAAACGTCTGATGTGACACCTAA

Reverse complement sequence

TTAGGTGTCACATCAGACGTTTGACCGAATGTCGGAAGGGGTTTTCGGACACGAATGAAAAAACTAATTTCAGAACTCGCCTGGAAACCGCGAGACGAAT[A/C]
TTTTGAGCCTACTTAAGCTGGCATTAGCACATGTGGGTTACTGTAGCACTTATGGCTAATCATGGCCTAATTAGGCTCAAAAGATTCGTCTCGCGATTTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	18.90%	17.80%	0.53%	62.82%	NA
All Indica	2759	2.90%	4.20%	0.65%	92.24%	NA
All Japonica	1512	50.00%	45.20%	0.26%	4.56%	NA
Aus	269	1.90%	1.90%	0.74%	95.54%	NA
Indica I	595	3.00%	0.70%	1.51%	94.79%	NA
Indica II	465	3.70%	1.70%	0.65%	93.98%	NA
Indica III	913	1.20%	5.60%	0.11%	93.10%	NA
Indica Intermediate	786	4.30%	6.70%	0.64%	88.30%	NA
Temperate Japonica	767	70.80%	23.10%	0.52%	5.61%	NA
Tropical Japonica	504	27.80%	68.30%	0.00%	3.97%	NA
Japonica Intermediate	241	30.30%	67.20%	0.00%	2.49%	NA
VI/Aromatic	96	22.90%	8.30%	1.04%	67.71%	NA
Intermediate	90	32.20%	31.10%	0.00%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207888547	T -> DEL	N	N	silent_mutation	Average:15.424; most accessible tissue: Callus, score: 74.87	N	N	N	N
vg1207888547	T -> G	LOC_Os12g13910.1	upstream_gene_variant ; 3828.0bp to feature; MODIFIER	silent_mutation	Average:15.424; most accessible tissue: Callus, score: 74.87	N	N	N	N
vg1207888547	T -> G	LOC_Os12g13900-LOC_Os12g13910	intergenic_region ; MODIFIER	silent_mutation	Average:15.424; most accessible tissue: Callus, score: 74.87	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207888547	NA	2.24E-10	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
vg1207888547	NA	3.57E-11	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
vg1207888547	2.50E-12	3.29E-18	mr1002	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
vg1207888547	3.28E-10	4.89E-19	mr1002	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
vg1207888547	NA	2.11E-12	mr1031	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
vg1207888547	NA	3.18E-06	mr1942	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
vg1207888547	1.07E-21	8.79E-29	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
vg1207888547	3.01E-19	1.20E-32	mr1002_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
vg1207888547	NA	1.07E-12	mr1011_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
vg1207888547	NA	3.42E-08	mr1011_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
vg1207888547	NA	2.79E-07	mr1013_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
vg1207888547	NA	6.73E-08	mr1031_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
vg1207888547	NA	5.83E-06	mr1330_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
vg1207888547	NA	3.20E-06	mr1865_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
vg1207888547	NA	8.43E-07	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