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Detailed information for vg0132244134:

Variant ID: vg0132244134 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 32244134
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.87, C: 0.13, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

CGATGTTCATTTCCTTATCCATGATAAGGATCTGCACACACTTAGGCTAAAAGTAAGCCAGAAGGTTTCAAAGTTATAAGCTAGATTTGCTATAACAAAG[A/C]
TATATATATTATCAGTGTGTTTCAAAGTGCCTATTTTATGTGCAACTTGTTAATCACTTTCCTAACTGTGCTGCCTTTCTGACCCTTCATTACTGTTGGG

Reverse complement sequence

CCCAACAGTAATGAAGGGTCAGAAAGGCAGCACAGTTAGGAAAGTGATTAACAAGTTGCACATAAAATAGGCACTTTGAAACACACTGATAATATATATA[T/G]
CTTTGTTATAGCAAATCTAGCTTATAACTTTGAAACCTTCTGGCTTACTTTTAGCCTAAGTGTGTGCAGATCCTTATCATGGATAAGGAAATGAACATCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.60%	31.60%	5.78%	28.95%	NA
All Indica	2759	10.90%	51.30%	6.09%	31.71%	NA
All Japonica	1512	69.40%	0.00%	4.76%	25.86%	NA
Aus	269	74.70%	24.50%	0.37%	0.37%	NA
Indica I	595	20.70%	12.40%	20.50%	46.39%	NA
Indica II	465	10.80%	26.50%	1.94%	60.86%	NA
Indica III	913	1.60%	90.80%	0.66%	6.90%	NA
Indica Intermediate	786	14.50%	49.40%	3.94%	32.19%	NA
Temperate Japonica	767	98.70%	0.00%	0.13%	1.17%	NA
Tropical Japonica	504	15.70%	0.00%	12.50%	71.83%	NA
Japonica Intermediate	241	88.40%	0.00%	3.32%	8.30%	NA
VI/Aromatic	96	6.20%	1.00%	21.88%	70.83%	NA
Intermediate	90	35.60%	15.60%	12.22%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0132244134	A -> DEL	N	N	silent_mutation	Average:45.736; most accessible tissue: Minghui63 flag leaf, score: 74.563	N	N	N	N
vg0132244134	A -> C	LOC_Os01g55990.1	upstream_gene_variant ; 3410.0bp to feature; MODIFIER	silent_mutation	Average:45.736; most accessible tissue: Minghui63 flag leaf, score: 74.563	N	N	N	N
vg0132244134	A -> C	LOC_Os01g56000.1	intron_variant ; MODIFIER	silent_mutation	Average:45.736; most accessible tissue: Minghui63 flag leaf, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0132244134	NA	1.24E-12	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
vg0132244134	NA	1.30E-16	Heading_date	Ind_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
vg0132244134	NA	1.07E-07	mr1870	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
vg0132244134	NA	6.07E-09	mr1221_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
vg0132244134	NA	6.41E-07	mr1583_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
vg0132244134	NA	7.31E-09	mr1870_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
vg0132244134	NA	2.96E-06	mr1971_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