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Detailed information for vg1013682143:

Variant ID: vg1013682143 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13682143
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TGACGGTAGACAACAATTTATTCCGTAAAGCCTATTTCACGGTTCTGCAACAATCTTCATTGGTGGCTCCTTACATCGAGGAGCACTTGGCTCTAGTTCG[T/C]
GCCAGAAACATCGGTAAGTCCGATGCATGGATTACACGGCATCACATTGATACTTTCTCCGCGTGGCTGCGACATCTCATGGGTAACGAGACGATTAACC

Reverse complement sequence

GGTTAATCGTCTCGTTACCCATGAGATGTCGCAGCCACGCGGAGAAAGTATCAATGTGATGCCGTGTAATCCATGCATCGGACTTACCGATGTTTCTGGC[A/G]
CGAACTAGAGCCAAGTGCTCCTCGATGTAAGGAGCCACCAATGAAGATTGTTGCAGAACCGTGAAATAGGCTTTACGGAATAAATTGTTGTCTACCGTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.00%	0.30%	1.69%	73.97%	NA
All Indica	2759	2.80%	0.60%	2.25%	94.35%	NA
All Japonica	1512	61.60%	0.00%	0.46%	37.90%	NA
Aus	269	3.70%	0.00%	2.60%	93.68%	NA
Indica I	595	2.20%	0.80%	4.03%	92.94%	NA
Indica II	465	5.20%	1.30%	0.65%	92.90%	NA
Indica III	913	0.90%	0.20%	1.20%	97.70%	NA
Indica Intermediate	786	4.20%	0.40%	3.05%	92.37%	NA
Temperate Japonica	767	93.90%	0.00%	0.00%	6.13%	NA
Tropical Japonica	504	20.60%	0.00%	0.79%	78.57%	NA
Japonica Intermediate	241	44.80%	0.00%	1.24%	53.94%	NA
VI/Aromatic	96	80.20%	0.00%	2.08%	17.71%	NA
Intermediate	90	41.10%	0.00%	2.22%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1013682143	T -> C	LOC_Os10g26370.1	synonymous_variant ; p.Arg738Arg; LOW	synonymous_codon	Average:14.618; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg1013682143	T -> DEL	LOC_Os10g26370.1	N	frameshift_variant	Average:14.618; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013682143	5.60E-07	NA	mr1317	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