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Detailed information for vg1207040173:

Variant ID: vg1207040173 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7040173
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTAAATTTAAATATAATTTGGCCGTAAATTACTTTTAAATTATTTATTAGAAATTCTTGCAGGTACATATATTGGAAGATTATCAAGCATTTGGTACT[G/A]
AGAAATCTACTTATATTGCATAAATCAAAAGTGTTGCCAAAATATATATATTACAATATTGTTTTACATTGTCACTTCAAATAACATCATCTAGTTACAT

Reverse complement sequence

ATGTAACTAGATGATGTTATTTGAAGTGACAATGTAAAACAATATTGTAATATATATATTTTGGCAACACTTTTGATTTATGCAATATAAGTAGATTTCT[C/T]
AGTACCAAATGCTTGATAATCTTCCAATATATGTACCTGCAAGAATTTCTAATAAATAATTTAAAAGTAATTTACGGCCAAATTATATTTAAATTTAAAT

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	50.70%	23.90%	2.48%	22.94%	NA
All Indica	2759	57.20%	39.20%	2.03%	1.59%	NA
All Japonica	1512	34.30%	1.50%	3.17%	61.04%	NA
Aus	269	71.40%	0.70%	1.86%	26.02%	NA
Indica I	595	88.40%	7.20%	3.19%	1.18%	NA
Indica II	465	28.80%	66.90%	2.37%	1.94%	NA
Indica III	913	48.00%	50.80%	0.55%	0.66%	NA
Indica Intermediate	786	60.90%	33.60%	2.67%	2.80%	NA
Temperate Japonica	767	38.10%	0.80%	2.74%	58.41%	NA
Tropical Japonica	504	17.90%	3.00%	4.76%	74.40%	NA
Japonica Intermediate	241	56.80%	0.40%	1.24%	41.49%	NA
VI/Aromatic	96	74.00%	4.20%	4.17%	17.71%	NA
Intermediate	90	42.20%	20.00%	4.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207040173	G -> DEL	N	N	silent_mutation	Average:30.452; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg1207040173	G -> A	LOC_Os12g12770.1	intron_variant ; MODIFIER	silent_mutation	Average:30.452; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207040173	NA	1.73E-10	Grain_width	Ind_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
vg1207040173	NA	7.95E-06	mr1069	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
vg1207040173	NA	6.34E-09	mr1174	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
vg1207040173	NA	5.00E-12	mr1180	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
vg1207040173	NA	1.50E-07	mr1180	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
vg1207040173	NA	5.88E-06	mr1531	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
vg1207040173	NA	2.96E-08	mr1557	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
vg1207040173	NA	4.35E-13	mr1565	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
vg1207040173	NA	3.53E-10	mr1565	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
vg1207040173	NA	3.36E-06	mr1944	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
vg1207040173	NA	2.50E-08	mr1024_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
vg1207040173	NA	1.14E-06	mr1094_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
vg1207040173	NA	2.45E-06	mr1278_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
vg1207040173	NA	2.03E-06	mr1497_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
vg1207040173	NA	4.71E-07	mr1508_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
vg1207040173	NA	2.22E-20	mr1565_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
vg1207040173	NA	1.33E-16	mr1565_2	Ind_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
vg1207040173	NA	9.29E-06	mr1733_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
vg1207040173	NA	1.85E-09	mr1861_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