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Detailed information for vg0721415805:

Variant ID: vg0721415805 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21415805
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.52, C: 0.49, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTAGCCCTTGGTTTGAACCCTTTGCCAGCCTCTTCACGGCTACCTCTTGTCCAAAAAGAAGTCCCTGAATAATTCTTAGTTTATTAGCTAATTTGCTT[T/C]
ATACATGGAGATATGGACAGAAATGGTGAATTTTGTAATGACTTAAGACTCTAACATGCATATGCTACTAATTTACAATATTTGGTTTTTCCAATAAAGC

Reverse complement sequence

GCTTTATTGGAAAAACCAAATATTGTAAATTAGTAGCATATGCATGTTAGAGTCTTAAGTCATTACAAAATTCACCATTTCTGTCCATATCTCCATGTAT[A/G]
AAGCAAATTAGCTAATAAACTAAGAATTATTCAGGGACTTCTTTTTGGACAAGAGGTAGCCGTGAAGAGGCTGGCAAAGGGTTCAAACCAAGGGCTAGAA

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	54.60%	25.90%	0.61%	18.90%	NA
All Indica	2759	50.70%	19.00%	0.94%	29.29%	NA
All Japonica	1512	70.10%	29.60%	0.07%	0.20%	NA
Aus	269	15.20%	59.50%	0.37%	24.91%	NA
Indica I	595	21.20%	9.10%	1.85%	67.90%	NA
Indica II	465	69.20%	17.00%	0.65%	13.12%	NA
Indica III	913	52.40%	30.70%	0.33%	16.65%	NA
Indica Intermediate	786	60.30%	14.20%	1.15%	24.30%	NA
Temperate Japonica	767	57.50%	42.50%	0.00%	0.00%	NA
Tropical Japonica	504	87.90%	11.90%	0.20%	0.00%	NA
Japonica Intermediate	241	73.00%	25.70%	0.00%	1.24%	NA
VI/Aromatic	96	33.30%	61.50%	0.00%	5.21%	NA
Intermediate	90	51.10%	36.70%	1.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0721415805	T -> DEL	N	N	silent_mutation	Average:34.204; most accessible tissue: Callus, score: 75.559	N	N	N	N
vg0721415805	T -> C	LOC_Os07g35740.1	upstream_gene_variant ; 4118.0bp to feature; MODIFIER	silent_mutation	Average:34.204; most accessible tissue: Callus, score: 75.559	N	N	N	N
vg0721415805	T -> C	LOC_Os07g35750.1	intron_variant ; MODIFIER	silent_mutation	Average:34.204; most accessible tissue: Callus, score: 75.559	N	N	N	N
vg0721415805	T -> C	LOC_Os07g35750.2	intron_variant ; MODIFIER	silent_mutation	Average:34.204; most accessible tissue: Callus, score: 75.559	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721415805	NA	8.98E-06	Grain_weight	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
vg0721415805	4.02E-06	3.94E-06	mr1218	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0721415805	NA	1.67E-06	mr1510_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