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Detailed information for vg1005523151:

Variant ID: vg1005523151 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5523151
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAATTCATAAGAAGCTTGGATGTTTCTTCCTTGATGAATGCCAACAGGAAGGATACATGGGCTGATTGCAGCTGAGAAGATTTCTCTGGATGATTGGTA[C/T]
ACTTCATGGTTGATGTCTTCGAATCTGAAGTCCACTGGGTGCTCAAGTTGTGCAGAGTCTTCATAAAGGAACCAGATTCTAGCATCTTTCTGAAAGCCTT

Reverse complement sequence

AAGGCTTTCAGAAAGATGCTAGAATCTGGTTCCTTTATGAAGACTCTGCACAACTTGAGCACCCAGTGGACTTCAGATTCGAAGACATCAACCATGAAGT[G/A]
TACCAATCATCCAGAGAAATCTTCTCAGCTGCAATCAGCCCATGTATCCTTCCTGTTGGCATTCATCAAGGAAGAAACATCCAAGCTTCTTATGAATTTT

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	75.10%	0.50%	3.77%	20.63%	NA
All Indica	2759	81.60%	0.70%	5.15%	12.58%	NA
All Japonica	1512	73.10%	0.10%	1.19%	25.60%	NA
Aus	269	16.70%	0.00%	6.32%	76.95%	NA
Indica I	595	99.20%	0.00%	0.17%	0.67%	NA
Indica II	465	84.10%	0.90%	3.87%	11.18%	NA
Indica III	913	69.80%	1.40%	8.76%	20.04%	NA
Indica Intermediate	786	80.40%	0.40%	5.47%	13.74%	NA
Temperate Japonica	767	86.20%	0.00%	0.52%	13.30%	NA
Tropical Japonica	504	56.50%	0.00%	2.18%	41.27%	NA
Japonica Intermediate	241	66.40%	0.40%	1.24%	31.95%	NA
VI/Aromatic	96	80.20%	0.00%	0.00%	19.79%	NA
Intermediate	90	81.10%	1.10%	1.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005523151	C -> T	LOC_Os10g10110.1	synonymous_variant ; p.Val250Val; LOW	synonymous_codon	Average:25.724; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N
vg1005523151	C -> DEL	LOC_Os10g10110.1	N	frameshift_variant	Average:25.724; most accessible tissue: Zhenshan97 flag leaf, score: 63.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005523151	5.16E-07	1.01E-09	mr1261	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