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Detailed information for vg1215874878:

Variant ID: vg1215874878 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15874878
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTCAAGGTGGAATTTTTTCCATCCGAATTTGTCTTGCCCATCTGCTTACCCATCTTGCCTATATGGACGTGACTAGGTAGAGTGCGGGTTCAGATCTC[C/G]
TGGAGTTGTGGACGACCCCACCAGGTGGATTTGGCCAAATATAGACCCTCCTTTTCTTCTACGGCTGAGATCATATCTCTTAATAATTATTATAAAAAAA

Reverse complement sequence

TTTTTTTATAATAATTATTAAGAGATATGATCTCAGCCGTAGAAGAAAAGGAGGGTCTATATTTGGCCAAATCCACCTGGTGGGGTCGTCCACAACTCCA[G/C]
GAGATCTGAACCCGCACTCTACCTAGTCACGTCCATATAGGCAAGATGGGTAAGCAGATGGGCAAGACAAATTCGGATGGAAAAAATTCCACCTTGAAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.50%	0.70%	0.55%	9.29%	NA
All Indica	2759	93.10%	0.10%	0.22%	6.56%	NA
All Japonica	1512	85.00%	1.90%	1.06%	12.04%	NA
Aus	269	72.90%	0.00%	1.49%	25.65%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	74.40%	0.00%	0.22%	25.38%	NA
Indica III	913	97.30%	0.00%	0.22%	2.52%	NA
Indica Intermediate	786	94.50%	0.00%	0.38%	5.09%	NA
Temperate Japonica	767	95.30%	2.60%	1.83%	0.26%	NA
Tropical Japonica	504	66.50%	0.60%	0.40%	32.54%	NA
Japonica Intermediate	241	90.90%	2.50%	0.00%	6.64%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	93.30%	0.00%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215874878	C -> DEL	N	N	silent_mutation	Average:30.462; most accessible tissue: Zhenshan97 flower, score: 69.437	N	N	N	N
vg1215874878	C -> G	LOC_Os12g27090-LOC_Os12g27096	intergenic_region ; MODIFIER	silent_mutation	Average:30.462; most accessible tissue: Zhenshan97 flower, score: 69.437	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215874878	9.19E-07	9.19E-07	mr1915	Jap_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
vg1215874878	1.74E-06	1.74E-06	mr1081_2	Jap_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
vg1215874878	NA	2.08E-06	mr1129_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
vg1215874878	NA	4.88E-06	mr1148_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
vg1215874878	NA	6.38E-06	mr1204_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
vg1215874878	NA	5.32E-06	mr1405_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
vg1215874878	NA	8.74E-06	mr1482_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
vg1215874878	NA	1.45E-06	mr1735_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