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Detailed information for vg0217694887:

Variant ID: vg0217694887 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17694887
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACATCTTTTCAAACCATTTTATCGAATAAATTATTTTGCAAAGCCAATTATTCATCACAAATATTAATCATGACAATGATTTCACAAACTACACTTAGT[G/A]
GGAATGAACTATATCAGTATATAGGATAAGTCACTTCGAATTTTTTTTCTAATCATCTTTTAGTTTGATCAAATTTATCGAAAAATTTGCAATAACAACA

Reverse complement sequence

TGTTGTTATTGCAAATTTTTCGATAAATTTGATCAAACTAAAAGATGATTAGAAAAAAAATTCGAAGTGACTTATCCTATATACTGATATAGTTCATTCC[C/T]
ACTAAGTGTAGTTTGTGAAATCATTGTCATGATTAATATTTGTGATGAATAATTGGCTTTGCAAAATAATTTATTCGATAAAATGGTTTGAAAAGATGTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.90%	2.00%	5.29%	47.74%	NA
All Indica	2759	21.90%	0.10%	7.61%	70.39%	NA
All Japonica	1512	91.80%	6.10%	0.79%	1.32%	NA
Aus	269	20.10%	0.00%	6.32%	73.61%	NA
Indica I	595	30.90%	0.20%	21.18%	47.73%	NA
Indica II	465	27.70%	0.00%	7.53%	64.73%	NA
Indica III	913	11.40%	0.00%	0.77%	87.84%	NA
Indica Intermediate	786	23.90%	0.10%	5.34%	70.61%	NA
Temperate Japonica	767	88.50%	9.30%	1.17%	1.04%	NA
Tropical Japonica	504	98.20%	0.00%	0.20%	1.59%	NA
Japonica Intermediate	241	88.80%	8.70%	0.83%	1.66%	NA
VI/Aromatic	96	28.10%	0.00%	1.04%	70.83%	NA
Intermediate	90	55.60%	2.20%	11.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0217694887	G -> A	LOC_Os02g29740.1	upstream_gene_variant ; 2640.0bp to feature; MODIFIER	silent_mutation	Average:30.807; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0217694887	G -> A	LOC_Os02g29750.1	intron_variant ; MODIFIER	silent_mutation	Average:30.807; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0217694887	G -> DEL	N	N	silent_mutation	Average:30.807; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217694887	2.20E-06	NA	Grain_length	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