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Detailed information for vg0622856929:

Variant ID: vg0622856929 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22856929
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, C: 0.10, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

CGGCTGCGTAGTAGGCGTCAGCTCCTGCGGCTGGATTGGATGGGGGATTATCTTATGGATCAGTGAGTGTCGATGAGCGTCAATTGTTTTGGTGGTTTTA[T/C]
GTCGTCGGTATCACGGGTGCAATAATGCGACGCTGGTTGATTCGTGAACAAAATATATACTGGGTAAGGACATGGGTTTTAGAGGTGGTACGTGTGCAGT

Reverse complement sequence

ACTGCACACGTACCACCTCTAAAACCCATGTCCTTACCCAGTATATATTTTGTTCACGAATCAACCAGCGTCGCATTATTGCACCCGTGATACCGACGAC[A/G]
TAAAACCACCAAAACAATTGACGCTCATCGACACTCACTGATCCATAAGATAATCCCCCATCCAATCCAGCCGCAGGAGCTGACGCCTACTACGCAGCCG

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	58.80%	34.70%	2.41%	4.04%	NA
All Indica	2759	80.00%	10.30%	3.77%	5.91%	NA
All Japonica	1512	15.70%	83.10%	0.20%	0.99%	NA
Aus	269	90.00%	4.50%	1.86%	3.72%	NA
Indica I	595	85.00%	0.80%	10.08%	4.03%	NA
Indica II	465	83.00%	7.10%	3.01%	6.88%	NA
Indica III	913	73.30%	18.80%	0.88%	7.01%	NA
Indica Intermediate	786	82.30%	9.40%	2.80%	5.47%	NA
Temperate Japonica	767	18.10%	80.20%	0.26%	1.43%	NA
Tropical Japonica	504	9.10%	90.30%	0.00%	0.60%	NA
Japonica Intermediate	241	21.60%	77.60%	0.41%	0.41%	NA
VI/Aromatic	96	52.10%	47.90%	0.00%	0.00%	NA
Intermediate	90	46.70%	47.80%	2.22%	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
vg0622856929	T -> C	LOC_Os06g38580.1	upstream_gene_variant ; 314.0bp to feature; MODIFIER	silent_mutation	Average:45.208; most accessible tissue: Callus, score: 89.701	N	N	N	N
vg0622856929	T -> C	LOC_Os06g38580-LOC_Os06g38590	intergenic_region ; MODIFIER	silent_mutation	Average:45.208; most accessible tissue: Callus, score: 89.701	N	N	N	N
vg0622856929	T -> DEL	N	N	silent_mutation	Average:45.208; most accessible tissue: Callus, score: 89.701	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622856929	5.36E-07	1.08E-08	Yield	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
vg0622856929	NA	2.21E-07	mr1973_2	Ind_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