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Detailed information for vg1117529722:

Variant ID: vg1117529722 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17529722
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTATATCATATTACCTACTTTTGGTAATTTGATTTAGGATATTGATTTTCAGTAATTCATTATTCTCTGCCATTTCATAATCCTTTCTACCCTATGGTGT[T/G]
TGATTATGAAAATTAAGATTTATTTGTATGTGATTAATTAAGCCAATGGAAATTAATTGCATTACTAATGTTTAATTAATAATTAATTTTTCAGCATTAG

Reverse complement sequence

CTAATGCTGAAAAATTAATTATTAATTAAACATTAGTAATGCAATTAATTTCCATTGGCTTAATTAATCACATACAAATAAATCTTAATTTTCATAATCA[A/C]
ACACCATAGGGTAGAAAGGATTATGAAATGGCAGAGAATAATGAATTACTGAAAATCAATATCCTAAATCAAATTACCAAAAGTAGGTAATATGATATAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.40%	0.00%	0.06%	1.48%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.04%	NA
All Japonica	1512	95.30%	0.00%	0.13%	4.56%	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%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.00%	0.13%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	88.30%	0.00%	0.20%	11.51%	NA
Japonica Intermediate	241	96.70%	0.00%	0.41%	2.90%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1117529722	T -> DEL	N	N	silent_mutation	Average:15.343; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1117529722	T -> G	LOC_Os11g30150.1	intron_variant ; MODIFIER	silent_mutation	Average:15.343; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117529722	4.98E-06	NA	Heading_date	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