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Detailed information for vg0901150996:

Variant ID: vg0901150996 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1150996
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

GCTAAGTACAATAGGCATCCATCCCACATGACATTCTAAAATAATGATCAATCTTGTATGTATGAACTGCGTTGCTCTTGATCTGACGAAACCTCGGCAA[C/T]
CATTTTGAAATAAACTGGATCACTAGAACTGACGGAATCTAAATGACAAACAAAGCATACATGAAATACAAGCAATAAGGCTACTGAAACAGCAAAAGAA

Reverse complement sequence

TTCTTTTGCTGTTTCAGTAGCCTTATTGCTTGTATTTCATGTATGCTTTGTTTGTCATTTAGATTCCGTCAGTTCTAGTGATCCAGTTTATTTCAAAATG[G/A]
TTGCCGAGGTTTCGTCAGATCAAGAGCAACGCAGTTCATACATACAAGATTGATCATTATTTTAGAATGTCATGTGGGATGGATGCCTATTGTACTTAGC

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	96.30%	3.70%	0.06%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	88.40%	11.40%	0.20%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	97.40%	2.30%	0.26%	0.00%	NA
Tropical Japonica	504	77.40%	22.60%	0.00%	0.00%	NA
Japonica Intermediate	241	83.00%	16.60%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0901150996	C -> T	LOC_Os09g02640.1	upstream_gene_variant ; 3534.0bp to feature; MODIFIER	silent_mutation	Average:37.19; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0901150996	C -> T	LOC_Os09g02640-LOC_Os09g02650	intergenic_region ; MODIFIER	silent_mutation	Average:37.19; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901150996	1.74E-06	NA	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