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Detailed information for vg0801634584:

Variant ID: vg0801634584 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1634584
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.04, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTCGATCAGATTCAGAGATGGCATCGTCTCGCCCCATCTCGGAGAGCACCATCACGAGGTCGACGTGCGCGACGCGGACGGCGCGCGCCACGCACCAG[T/C]
TCGAGATCGTCGGGTACAGCCTCAAGAGGTGCCTCGCCGCCGGCGAGTTCGTCCGGTCCTCCGCCTTCGCCGCCTGCGGCTACAGGTGGTCCGTCCGCGT

Reverse complement sequence

ACGCGGACGGACCACCTGTAGCCGCAGGCGGCGAAGGCGGAGGACCGGACGAACTCGCCGGCGGCGAGGCACCTCTTGAGGCTGTACCCGACGATCTCGA[A/G]
CTGGTGCGTGGCGCGCGCCGTCCGCGTCGCGCACGTCGACCTCGTGATGGTGCTCTCCGAGATGGGGCGAGACGATGCCATCTCTGAATCTGATCGAGCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.50%	9.70%	0.08%	0.72%	NA
All Indica	2759	85.20%	13.40%	0.11%	1.23%	NA
All Japonica	1512	95.00%	5.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.30%	1.30%	0.00%	2.35%	NA
Indica II	465	90.50%	9.50%	0.00%	0.00%	NA
Indica III	913	77.90%	21.20%	0.11%	0.77%	NA
Indica Intermediate	786	82.20%	15.90%	0.25%	1.65%	NA
Temperate Japonica	767	94.70%	5.20%	0.13%	0.00%	NA
Tropical Japonica	504	93.70%	6.30%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg0801634584	T -> C	LOC_Os08g03490.1	missense_variant ; p.Phe28Leu; MODERATE	nonsynonymous_codon ; F28L	Average:71.703; most accessible tissue: Minghui63 root, score: 79.522	unknown	unknown	TOLERATED	0.06
vg0801634584	T -> DEL	LOC_Os08g03490.1	N	frameshift_variant	Average:71.703; most accessible tissue: Minghui63 root, score: 79.522	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801634584	NA	3.30E-08	Awn_length	Ind_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