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Detailed information for vg0120457787:

Variant ID: vg0120457787 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 20457787
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAAGAGAGCCGAGACTGAGCTTTCGTTTGGCACCCACCCTTGAGGGGCGAGGCCGTTAGGTGTATGTTGTGCCATTCAATGGGAAACATATTGCACGC[T/G]
CCACATGCTCGCGTGCAAATTAACCGCCGGTGCTCATGGGTAAGGGATACCACACAGTACACCGTGATTGTTTTGCCGGTTCATCCAGGAGATGTAGTGC

Reverse complement sequence

GCACTACATCTCCTGGATGAACCGGCAAAACAATCACGGTGTACTGTGTGGTATCCCTTACCCATGAGCACCGGCGGTTAATTTGCACGCGAGCATGTGG[A/C]
GCGTGCAATATGTTTCCCATTGAATGGCACAACATACACCTAACGGCCTCGCCCCTCAAGGGTGGGTGCCAAACGAAAGCTCAGTCTCGGCTCTCTTTGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.40%	8.50%	6.92%	0.17%	NA
All Indica	2759	95.60%	0.90%	3.44%	0.04%	NA
All Japonica	1512	61.70%	23.50%	14.35%	0.40%	NA
Aus	269	95.50%	0.70%	3.72%	0.00%	NA
Indica I	595	95.80%	0.70%	3.36%	0.17%	NA
Indica II	465	96.80%	1.70%	1.51%	0.00%	NA
Indica III	913	99.10%	0.10%	0.77%	0.00%	NA
Indica Intermediate	786	90.60%	1.70%	7.76%	0.00%	NA
Temperate Japonica	767	38.60%	39.50%	21.25%	0.65%	NA
Tropical Japonica	504	93.50%	1.20%	5.36%	0.00%	NA
Japonica Intermediate	241	68.90%	19.50%	11.20%	0.41%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	78.90%	14.40%	5.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0120457787	T -> G	LOC_Os01g36780-LOC_Os01g36790	intergenic_region ; MODIFIER	silent_mutation	Average:79.369; most accessible tissue: Zhenshan97 panicle, score: 86.788	N	N	N	N
vg0120457787	T -> DEL	N	N	silent_mutation	Average:79.369; most accessible tissue: Zhenshan97 panicle, score: 86.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0120457787	NA	2.72E-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
vg0120457787	NA	1.15E-07	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
vg0120457787	NA	5.23E-07	mr1013	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
vg0120457787	NA	6.81E-07	mr1031	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
vg0120457787	1.69E-06	8.25E-14	mr1034	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
vg0120457787	NA	8.49E-06	mr1034	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
vg0120457787	NA	2.52E-06	mr1056	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
vg0120457787	5.65E-06	NA	mr1163	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
vg0120457787	NA	3.97E-09	mr1163	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
vg0120457787	NA	9.51E-07	mr1252	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
vg0120457787	8.69E-06	4.36E-08	mr1343	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
vg0120457787	5.58E-06	5.58E-06	mr1343	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
vg0120457787	NA	1.37E-06	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
vg0120457787	NA	8.69E-06	mr1829_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
vg0120457787	NA	3.99E-06	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