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Detailed information for vg0402811414:

Variant ID: vg0402811414 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2811414
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, C: 0.03, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

AGATTGCTTGCAAGAAAGACGAGAATAGCTATGCACAAGTCTGGGAAAGGTACATCGACAAAACTCTGATGCAGGCTGCTGACGATAGGTTACAAGGTGC[G/C]
TTCGATAAGAGGCAGATGGAGCGTGTGATCGTCTTGGGGCTGTGGTGTTGTCAGCCTAATATTGAGATGCGACCTACGATGGAGAAAGCAATGGATTTCC

Reverse complement sequence

GGAAATCCATTGCTTTCTCCATCGTAGGTCGCATCTCAATATTAGGCTGACAACACCACAGCCCCAAGACGATCACACGCTCCATCTGCCTCTTATCGAA[C/G]
GCACCTTGTAACCTATCGTCAGCAGCCTGCATCAGAGTTTTGTCGATGTACCTTTCCCAGACTTGTGCATAGCTATTCTCGTCTTTCTTGCAAGCAATCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.10%	3.60%	0.30%	3.07%	NA
All Indica	2759	98.20%	1.30%	0.00%	0.54%	NA
All Japonica	1512	85.10%	5.60%	0.93%	8.33%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	96.10%	3.00%	0.00%	0.99%	NA
Indica Intermediate	786	98.20%	1.00%	0.00%	0.76%	NA
Temperate Japonica	767	82.50%	9.90%	1.83%	5.74%	NA
Tropical Japonica	504	92.70%	0.60%	0.00%	6.75%	NA
Japonica Intermediate	241	77.60%	2.50%	0.00%	19.92%	NA
VI/Aromatic	96	58.30%	40.60%	0.00%	1.04%	NA
Intermediate	90	87.80%	8.90%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402811414	G -> C	LOC_Os04g05560.1	synonymous_variant ; p.Ala586Ala; LOW	synonymous_codon	Average:63.864; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0402811414	G -> DEL	LOC_Os04g05560.1	N	frameshift_variant	Average:63.864; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402811414	4.36E-10	8.67E-35	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
vg0402811414	NA	1.24E-11	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
vg0402811414	7.13E-06	NA	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
vg0402811414	NA	2.65E-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
vg0402811414	NA	2.64E-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