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Detailed information for vg0421937587:

Variant ID: vg0421937587 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21937587
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTGACTTGCCTTGCTCAAGGTCTTCACGAAGCTTCAGGAATCTTCGAGAAAACCCGCGATCGACGAAAATCCGGTAACCGCAACTATACGCAAACAAT[C/T]
GAAAACCTAAATAAAAGACCAAAAGAAGGATCCTATTTAGACTAATTAGTAGCGCCATTAAATAGATCTCAATTTTATGGAAATACTGGAAGTTGAACGG

Reverse complement sequence

CCGTTCAACTTCCAGTATTTCCATAAAATTGAGATCTATTTAATGGCGCTACTAATTAGTCTAAATAGGATCCTTCTTTTGGTCTTTTATTTAGGTTTTC[G/A]
ATTGTTTGCGTATAGTTGCGGTTACCGGATTTTCGTCGATCGCGGGTTTTCTCGAAGATTCCTGAAGCTTCGTGAAGACCTTGAGCAAGGCAAGTCACCC

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	86.60%	13.10%	0.30%	0.00%	NA
All Indica	2759	78.80%	20.70%	0.51%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	83.30%	16.70%	0.00%	0.00%	NA
Indica I	595	85.70%	14.30%	0.00%	0.00%	NA
Indica II	465	93.80%	6.20%	0.00%	0.00%	NA
Indica III	913	64.60%	34.00%	1.42%	0.00%	NA
Indica Intermediate	786	81.00%	18.80%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0421937587	C -> T	LOC_Os04g35970.1	upstream_gene_variant ; 4030.0bp to feature; MODIFIER	silent_mutation	Average:20.846; most accessible tissue: Zhenshan97 root, score: 30.989	N	N	N	N
vg0421937587	C -> T	LOC_Os04g35990.1	downstream_gene_variant ; 4612.0bp to feature; MODIFIER	silent_mutation	Average:20.846; most accessible tissue: Zhenshan97 root, score: 30.989	N	N	N	N
vg0421937587	C -> T	LOC_Os04g35980.1	intron_variant ; MODIFIER	silent_mutation	Average:20.846; most accessible tissue: Zhenshan97 root, score: 30.989	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421937587	9.25E-07	NA	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