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Detailed information for vg0627174899:

Variant ID: vg0627174899 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 27174899
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.70, C: 0.30, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAATAGAGGACTTATTTACCTTAACTTAGGTTGCAACTCAGAACAGCCCGAGAATGCAACCGACGACACAGACGAGGAAACACCAACAACAGCAGCAG[T/C]
GGCGGAACCAACGAACTAACACCCAAACACCACAGGCGATGGCTAGGAACCAGGACGAAACCCTAATCTTCACTTCACTTCATCTTCACTTTAAGGCGGA

Reverse complement sequence

TCCGCCTTAAAGTGAAGATGAAGTGAAGTGAAGATTAGGGTTTCGTCCTGGTTCCTAGCCATCGCCTGTGGTGTTTGGGTGTTAGTTCGTTGGTTCCGCC[A/G]
CTGCTGCTGTTGTTGGTGTTTCCTCGTCTGTGTCGTCGGTTGCATTCTCGGGCTGTTCTGAGTTGCAACCTAAGTTAAGGTAAATAAGTCCTCTATTTAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.60%	40.60%	0.78%	0.00%	NA
All Indica	2759	92.80%	6.50%	0.72%	0.00%	NA
All Japonica	1512	0.50%	99.40%	0.07%	0.00%	NA
Aus	269	56.90%	37.20%	5.95%	0.00%	NA
Indica I	595	97.30%	1.30%	1.34%	0.00%	NA
Indica II	465	93.10%	5.20%	1.72%	0.00%	NA
Indica III	913	88.80%	11.20%	0.00%	0.00%	NA
Indica Intermediate	786	93.80%	5.70%	0.51%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	0.00%	99.80%	0.20%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	46.70%	53.30%	0.00%	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
vg0627174899	T -> C	LOC_Os06g44940.1	upstream_gene_variant ; 4530.0bp to feature; MODIFIER	silent_mutation	Average:62.65; most accessible tissue: Minghui63 flower, score: 78.979	N	N	N	N
vg0627174899	T -> C	LOC_Os06g44930-LOC_Os06g44940	intergenic_region ; MODIFIER	silent_mutation	Average:62.65; most accessible tissue: Minghui63 flower, score: 78.979	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0627174899	NA	1.23E-18	Yield	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
vg0627174899	NA	2.47E-30	mr1086	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
vg0627174899	NA	5.99E-07	mr1103	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
vg0627174899	NA	2.85E-06	mr1107	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
vg0627174899	NA	7.30E-52	mr1154	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
vg0627174899	NA	6.33E-08	mr1154	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
vg0627174899	NA	6.54E-06	mr1246	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
vg0627174899	NA	1.90E-12	mr1751	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
vg0627174899	NA	1.04E-33	mr1878	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
vg0627174899	NA	4.44E-08	mr1246_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
vg0627174899	NA	6.82E-27	mr1323_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
vg0627174899	NA	4.99E-50	mr1404_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
vg0627174899	NA	2.98E-06	mr1404_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
vg0627174899	NA	5.33E-07	mr1620_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
vg0627174899	NA	5.43E-36	mr1878_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