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Detailed information for vg0601966864:

Variant ID: vg0601966864 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 1966864
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.28, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTAAAAGTGGTCACTTAAGCTGATCGCTCGTGGAAATGATGTTATTTCGACATTAAGCTGGCCGTCATTGAAATTTTATTTTTTCCAGGCTATGCTC[C/T]
TATTTATCTGCTTGAATCTTGTCTTGTCGTCTTCCTCACAACTCTTCGGTGATCGGCGCTTCAAAAATCAAGCCGTCGATCAAACGCTGGTCGCATCTCC

Reverse complement sequence

GGAGATGCGACCAGCGTTTGATCGACGGCTTGATTTTTGAAGCGCCGATCACCGAAGAGTTGTGAGGAAGACGACAAGACAAGATTCAAGCAGATAAATA[G/A]
GAGCATAGCCTGGAAAAAATAAAATTTCAATGACGGCCAGCTTAATGTCGAAATAACATCATTTCCACGAGCGATCAGCTTAAGTGACCACTTTTAAAAA

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	95.30%	4.60%	0.04%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.04%	0.00%	NA
All Japonica	1512	89.30%	10.70%	0.00%	0.00%	NA
Aus	269	85.50%	14.10%	0.37%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.70%	1.10%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	80.70%	19.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0601966864	C -> T	LOC_Os06g04540.1	upstream_gene_variant ; 3284.0bp to feature; MODIFIER	silent_mutation	Average:39.835; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0601966864	C -> T	LOC_Os06g04550.1	upstream_gene_variant ; 1761.0bp to feature; MODIFIER	silent_mutation	Average:39.835; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0601966864	C -> T	LOC_Os06g04540-LOC_Os06g04550	intergenic_region ; MODIFIER	silent_mutation	Average:39.835; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0601966864	1.28E-11	1.40E-24	Awn_length	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
vg0601966864	NA	1.77E-13	Awn_length	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
vg0601966864	NA	1.28E-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
vg0601966864	NA	2.81E-10	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
vg0601966864	NA	5.44E-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
vg0601966864	NA	9.15E-11	mr1624_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
vg0601966864	NA	1.12E-09	mr1741_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
vg0601966864	NA	1.49E-06	mr1757_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
vg0601966864	NA	5.90E-06	mr1788_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