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Detailed information for vg1003302932:

Variant ID: vg1003302932 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3302932
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGAGAATCCTTCAATAAACCTTCGGTAGTATCCGGCTAAGCCTATAAAACTCCGAATTTCAGTCACAAATTTGGGTGCTTTCCATTCCGTAACGGCCTC[A/C]
ACTTTAGCAGGATCCATTGCTACTCCACCGGCTGAGATTACGTGGCCTAGAAAAGCGACTTCTTTTAACCAGAACTCACATTTACTAAACTTTGCATATA

Reverse complement sequence

TATATGCAAAGTTTAGTAAATGTGAGTTCTGGTTAAAAGAAGTCGCTTTTCTAGGCCACGTAATCTCAGCCGGTGGAGTAGCAATGGATCCTGCTAAAGT[T/G]
GAGGCCGTTACGGAATGGAAAGCACCCAAATTTGTGACTGAAATTCGGAGTTTTATAGGCTTAGCCGGATACTACCGAAGGTTTATTGAAGGATTCTCTA

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	78.00%	0.10%	3.87%	18.09%	NA
All Indica	2759	70.00%	0.10%	3.95%	25.95%	NA
All Japonica	1512	88.90%	0.10%	2.98%	8.07%	NA
Aus	269	96.30%	0.00%	1.86%	1.86%	NA
Indica I	595	65.90%	0.20%	3.19%	30.76%	NA
Indica II	465	71.00%	0.20%	3.44%	25.38%	NA
Indica III	913	74.30%	0.00%	4.38%	21.36%	NA
Indica Intermediate	786	67.70%	0.00%	4.33%	27.99%	NA
Temperate Japonica	767	83.10%	0.10%	3.39%	13.43%	NA
Tropical Japonica	504	95.40%	0.00%	3.37%	1.19%	NA
Japonica Intermediate	241	93.80%	0.00%	0.83%	5.39%	NA
VI/Aromatic	96	76.00%	0.00%	19.79%	4.17%	NA
Intermediate	90	85.60%	0.00%	5.56%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003302932	A -> C	LOC_Os10g06430.1	synonymous_variant ; p.Val856Val; LOW	synonymous_codon	Average:13.502; most accessible tissue: Callus, score: 29.724	N	N	N	N
vg1003302932	A -> DEL	LOC_Os10g06430.1	N	frameshift_variant	Average:13.502; most accessible tissue: Callus, score: 29.724	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003302932	7.74E-07	1.19E-07	mr1698	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