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Detailed information for vg0721887753:

Variant ID: vg0721887753 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21887753
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATTACGCTTCTCAGCGGCCCGAACCTGTCTACATCGCCCGTGTCTTGTGCATTTGCTCTCTCGCGAACATTCCACAGATCGAGGGTGAAGAACCTCACT[T/C]
AGCGCCCCCGGCCGAACCGGCAAAGGGGGGTCTGCGCGGTCTCCCGGTGAGGAGCCCCACGCTCCGTCAGAGGGAGTATGTAATTTTAGTGTATTTACAA

Reverse complement sequence

TTGTAAATACACTAAAATTACATACTCCCTCTGACGGAGCGTGGGGCTCCTCACCGGGAGACCGCGCAGACCCCCCTTTGCCGGTTCGGCCGGGGGCGCT[A/G]
AGTGAGGTTCTTCACCCTCGATCTGTGGAATGTTCGCGAGAGAGCAAATGCACAAGACACGGGCGATGTAGACAGGTTCGGGCCGCTGAGAAGCGTAATA

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	82.00%	5.20%	12.53%	0.28%	NA
All Indica	2759	69.70%	8.70%	21.09%	0.47%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	96.30%	2.20%	1.49%	0.00%	NA
Indica I	595	92.60%	1.20%	6.22%	0.00%	NA
Indica II	465	53.50%	8.00%	37.20%	1.29%	NA
Indica III	913	63.10%	14.70%	21.47%	0.77%	NA
Indica Intermediate	786	69.70%	7.90%	22.39%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	2.20%	6.67%	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
vg0721887753	T -> DEL	N	N	silent_mutation	Average:18.828; most accessible tissue: Callus, score: 37.757	N	N	N	N
vg0721887753	T -> C	LOC_Os07g36590.1	upstream_gene_variant ; 4381.0bp to feature; MODIFIER	silent_mutation	Average:18.828; most accessible tissue: Callus, score: 37.757	N	N	N	N
vg0721887753	T -> C	LOC_Os07g36590-LOC_Os07g36600	intergenic_region ; MODIFIER	silent_mutation	Average:18.828; most accessible tissue: Callus, score: 37.757	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721887753	NA	8.17E-07	Grain_weight	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