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Detailed information for vg1016928784:

Variant ID: vg1016928784 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 16928784
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTACAACGCCATCATCGGGAGAACTGCACTTGCGAAGTTTATGGCCGCATCTCACTACGCGTATCAAGTGCTCAAGATGCTGGGACCGAAGGGAACAAT[C/T]
ACTATTCAAGGGAACGCAAAGCTGGCGGTACAATGCGACAAAAGGAGCCTCGACATGGTCGAGCAAACACCCAGCCCACCCGCCACAACTGAGCCACCCA

Reverse complement sequence

TGGGTGGCTCAGTTGTGGCGGGTGGGCTGGGTGTTTGCTCGACCATGTCGAGGCTCCTTTTGTCGCATTGTACCGCCAGCTTTGCGTTCCCTTGAATAGT[G/A]
ATTGTTCCCTTCGGTCCCAGCATCTTGAGCACTTGATACGCGTAGTGAGATGCGGCCATAAACTTCGCAAGTGCAGTTCTCCCGATGATGGCGTTGTAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.70%	27.40%	34.62%	3.34%	NA
All Indica	2759	21.90%	31.40%	42.77%	3.95%	NA
All Japonica	1512	63.40%	9.40%	24.27%	2.91%	NA
Aus	269	9.70%	72.10%	18.22%	0.00%	NA
Indica I	595	16.60%	29.20%	48.24%	5.88%	NA
Indica II	465	25.80%	20.00%	48.17%	6.02%	NA
Indica III	913	22.90%	39.80%	35.82%	1.53%	NA
Indica Intermediate	786	22.30%	30.20%	43.51%	4.07%	NA
Temperate Japonica	767	96.30%	0.40%	2.87%	0.39%	NA
Tropical Japonica	504	19.60%	22.80%	55.16%	2.38%	NA
Japonica Intermediate	241	50.20%	10.00%	27.80%	12.03%	NA
VI/Aromatic	96	9.40%	72.90%	17.71%	0.00%	NA
Intermediate	90	45.60%	23.30%	25.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1016928784	C -> T	LOC_Os10g32240.1	synonymous_variant ; p.Ile371Ile; LOW	synonymous_codon	Average:40.712; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg1016928784	C -> DEL	LOC_Os10g32240.1	N	frameshift_variant	Average:40.712; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1016928784	2.58E-06	2.58E-06	mr1260	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