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Detailed information for vg0115319961:

Variant ID: vg0115319961 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15319961
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGATGTCTGTCGAAACACCTCCCACCTCGTCGGGGCCCTAGGCGAAGATATCAATGTTTTTCTTGAGCACCTCCAGGATGTTCTCAACTTCTCTTTCGC[A/C]
CATGTCGCCCCCTAGAGATACAAGTCTTGTGGGATCGGCATCGTCGACCTGCACCTTGATCACCCTGCCATGAGGGGGTCATGCAGTTCGGCCTCAACAT

Reverse complement sequence

ATGTTGAGGCCGAACTGCATGACCCCCTCATGGCAGGGTGATCAAGGTGCAGGTCGACGATGCCGATCCCACAAGACTTGTATCTCTAGGGGGCGACATG[T/G]
GCGAAAGAGAAGTTGAGAACATCCTGGAGGTGCTCAAGAAAAACATTGATATCTTCGCCTAGGGCCCCGACGAGGTGGGAGGTGTTTCGACAGACATCAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.20%	1.80%	6.79%	57.22%	NA
All Indica	2759	6.00%	2.80%	6.92%	84.23%	NA
All Japonica	1512	85.60%	0.20%	2.98%	11.18%	NA
Aus	269	26.40%	0.70%	29.00%	43.87%	NA
Indica I	595	8.10%	0.20%	3.87%	87.90%	NA
Indica II	465	6.90%	11.00%	4.30%	77.85%	NA
Indica III	913	2.40%	0.20%	9.97%	87.40%	NA
Indica Intermediate	786	8.10%	3.10%	7.25%	81.55%	NA
Temperate Japonica	767	94.40%	0.00%	0.39%	5.22%	NA
Tropical Japonica	504	89.10%	0.00%	2.58%	8.33%	NA
Japonica Intermediate	241	50.60%	1.20%	12.03%	36.10%	NA
VI/Aromatic	96	37.50%	1.00%	2.08%	59.38%	NA
Intermediate	90	52.20%	2.20%	5.56%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115319961	A -> DEL	N	N	silent_mutation	Average:10.841; most accessible tissue: Callus, score: 36.908	N	N	N	N
vg0115319961	A -> C	LOC_Os01g27440.1	intron_variant ; MODIFIER	silent_mutation	Average:10.841; most accessible tissue: Callus, score: 36.908	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115319961	1.24E-06	1.24E-06	mr1040	Ind_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