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Detailed information for vg0507027003:

Variant ID: vg0507027003 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7027003
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, T: 0.07, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCACTCCGTTTCACAATGTAAGTCGTTCTAGCATTTTCCACATTCATATATCAATATGAATGTGGGAAATGCTAGAATGACTTATATTGTGAAACGGA[G/T]
GAAGTAACTAAGATCTATGTCTACTCTCCATGACTTGCCTCCACCTCAACAGATATTTCTTAATAGTGTAACAGCATTGTGATAAACAAAGATGGTTCAC

Reverse complement sequence

GTGAACCATCTTTGTTTATCACAATGCTGTTACACTATTAAGAAATATCTGTTGAGGTGGAGGCAAGTCATGGAGAGTAGACATAGATCTTAGTTACTTC[C/A]
TCCGTTTCACAATATAAGTCATTCTAGCATTTCCCACATTCATATTGATATATGAATGTGGAAAATGCTAGAACGACTTACATTGTGAAACGGAGTGAGT

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	54.50%	45.20%	0.32%	0.00%	NA
All Indica	2759	58.90%	40.80%	0.33%	0.00%	NA
All Japonica	1512	47.40%	52.30%	0.26%	0.00%	NA
Aus	269	29.00%	71.00%	0.00%	0.00%	NA
Indica I	595	22.70%	77.30%	0.00%	0.00%	NA
Indica II	465	86.70%	13.10%	0.22%	0.00%	NA
Indica III	913	68.10%	31.40%	0.44%	0.00%	NA
Indica Intermediate	786	59.00%	40.50%	0.51%	0.00%	NA
Temperate Japonica	767	15.90%	83.80%	0.26%	0.00%	NA
Tropical Japonica	504	89.30%	10.70%	0.00%	0.00%	NA
Japonica Intermediate	241	60.20%	39.00%	0.83%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	71.10%	26.70%	2.22%	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
vg0507027003	G -> T	LOC_Os05g12250-LOC_Os05g12260	intergenic_region ; MODIFIER	silent_mutation	Average:42.932; most accessible tissue: Callus, score: 61.936	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507027003	7.43E-08	NA	Grain_thickness	All	YES	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
vg0507027003	NA	3.85E-16	Grain_thickness	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
vg0507027003	3.54E-06	NA	Grain_weight	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
vg0507027003	NA	6.24E-06	mr1231	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
vg0507027003	2.07E-13	2.33E-37	mr1593	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
vg0507027003	1.23E-11	2.79E-26	mr1593	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
vg0507027003	NA	4.02E-21	mr1593	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
vg0507027003	NA	1.10E-06	mr1904	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
vg0507027003	NA	7.49E-07	mr1115_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
vg0507027003	NA	1.99E-12	mr1195_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
vg0507027003	NA	7.43E-06	mr1268_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
vg0507027003	NA	1.76E-09	mr1327_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
vg0507027003	NA	6.53E-06	mr1482_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
vg0507027003	NA	1.75E-08	mr1531_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
vg0507027003	1.20E-14	1.46E-42	mr1593_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
vg0507027003	3.57E-13	2.70E-28	mr1593_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
vg0507027003	1.35E-07	6.99E-29	mr1593_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
vg0507027003	NA	5.58E-06	mr1611_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
vg0507027003	NA	1.86E-06	mr1735_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
vg0507027003	NA	8.53E-14	mr1807_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