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Detailed information for vg0425995589:

Variant ID: vg0425995589 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 25995589
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

GGTTTGTGTTACCAACCGGGACTAAAGATCATCTTTAGTCCCGGTTCGAATGCTGTCAGGACCTGTCAGGCCCCCCCGGGATCTTTAGTCCCGGTTGGTA[T/A]
TACCAACCGGGACTAAAGTTCTTAACTTTAGTCCCGGTTGGTGTTACCAACCGGGACTAAAGATTCCGGTGTCCCGGTTGGTAATACCAACCGGGACTAA

Reverse complement sequence

TTAGTCCCGGTTGGTATTACCAACCGGGACACCGGAATCTTTAGTCCCGGTTGGTAACACCAACCGGGACTAAAGTTAAGAACTTTAGTCCCGGTTGGTA[A/T]
TACCAACCGGGACTAAAGATCCCGGGGGGGCCTGACAGGTCCTGACAGCATTCGAACCGGGACTAAAGATGATCTTTAGTCCCGGTTGGTAACACAAACC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.30%	36.30%	13.35%	13.06%	NA
All Indica	2759	35.10%	31.90%	14.72%	18.27%	NA
All Japonica	1512	37.80%	48.00%	8.93%	5.22%	NA
Aus	269	59.50%	20.40%	15.24%	4.83%	NA
Indica I	595	40.00%	35.80%	9.24%	14.96%	NA
Indica II	465	40.40%	19.80%	12.69%	27.10%	NA
Indica III	913	27.60%	37.60%	21.47%	13.36%	NA
Indica Intermediate	786	37.00%	29.50%	12.21%	21.25%	NA
Temperate Japonica	767	9.40%	81.00%	5.87%	3.78%	NA
Tropical Japonica	504	76.40%	8.30%	9.92%	5.36%	NA
Japonica Intermediate	241	47.70%	26.10%	16.60%	9.54%	NA
VI/Aromatic	96	32.30%	16.70%	36.46%	14.58%	NA
Intermediate	90	35.60%	41.10%	15.56%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0425995589	T -> DEL	N	N	silent_mutation	Average:28.317; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0425995589	T -> A	LOC_Os04g43890.1	upstream_gene_variant ; 799.0bp to feature; MODIFIER	silent_mutation	Average:28.317; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0425995589	T -> A	LOC_Os04g43880.1	downstream_gene_variant ; 2456.0bp to feature; MODIFIER	silent_mutation	Average:28.317; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0425995589	T -> A	LOC_Os04g43880-LOC_Os04g43890	intergenic_region ; MODIFIER	silent_mutation	Average:28.317; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0425995589	1.26E-06	9.26E-13	Grain_thickness	Jap_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
vg0425995589	NA	2.38E-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
vg0425995589	NA	4.71E-06	mr1077	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
vg0425995589	NA	9.55E-06	mr1177	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
vg0425995589	NA	1.10E-06	mr1330	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
vg0425995589	NA	5.57E-08	mr1952_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