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Detailed information for vg0215381884:

Variant ID: vg0215381884 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 15381884
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCAACGAGTGTACGAAGCTATAGTAAGTGTCTAGTCAAACTAGATGTTCGCATTGTTTCCCATTGTGCAGTTTATTTAACCCCACTAAATTGTAATGCA[A/G]
AAGGAGTTGGTTGCCAAGCAACAAGCCTCGCAAGAGGCCTGCTCTCAAAGACGCGAGGATGACGTCATCACGAAAGCGTTGGGCAACAAGGAACACCGTG

Reverse complement sequence

CACGGTGTTCCTTGTTGCCCAACGCTTTCGTGATGACGTCATCCTCGCGTCTTTGAGAGCAGGCCTCTTGCGAGGCTTGTTGCTTGGCAACCAACTCCTT[T/C]
TGCATTACAATTTAGTGGGGTTAAATAAACTGCACAATGGGAAACAATGCGAACATCTAGTTTGACTAGACACTTACTATAGCTTCGTACACTCGTTGAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.40%	0.10%	6.75%	24.74%	NA
All Indica	2759	52.30%	0.10%	10.33%	37.30%	NA
All Japonica	1512	98.30%	0.20%	0.46%	1.06%	NA
Aus	269	55.40%	0.00%	7.81%	36.80%	NA
Indica I	595	46.70%	0.00%	6.05%	47.23%	NA
Indica II	465	47.50%	0.00%	8.17%	44.30%	NA
Indica III	913	56.30%	0.30%	16.21%	27.16%	NA
Indica Intermediate	786	54.60%	0.00%	8.02%	37.40%	NA
Temperate Japonica	767	99.20%	0.10%	0.00%	0.65%	NA
Tropical Japonica	504	97.60%	0.00%	0.79%	1.59%	NA
Japonica Intermediate	241	96.70%	0.80%	1.24%	1.24%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	70.00%	0.00%	6.67%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0215381884	A -> G	LOC_Os02g26190.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:13.442; most accessible tissue: Callus, score: 26.41	N	N	N	N
vg0215381884	A -> G	LOC_Os02g26190.2	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:13.442; most accessible tissue: Callus, score: 26.41	N	N	N	N
vg0215381884	A -> DEL	N	N	silent_mutation	Average:13.442; most accessible tissue: Callus, score: 26.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0215381884	1.09E-06	NA	mr1595	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