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Detailed information for vg1013317545:

Variant ID: vg1013317545 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13317545
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCAGCTCCCGTTCACGTGTCAGCTCCCGCGTCCGCTCTCTCCTTCGCTCTAGCATCAGCCGCCAGGGGTCCAGCCAGTGGCAACGGAGGTTGGTTGTC[C/T]
GCTACTCCCAGTGGCAGCCGCGATCTCAGCAGCAGTAGCTCCAGTGGCTCAGAGTCGGGCAGCGGCGAGACTTATCTGCCAGGCTCCAGGAGTCGCTCAG

Reverse complement sequence

CTGAGCGACTCCTGGAGCCTGGCAGATAAGTCTCGCCGCTGCCCGACTCTGAGCCACTGGAGCTACTGCTGCTGAGATCGCGGCTGCCACTGGGAGTAGC[G/A]
GACAACCAACCTCCGTTGCCACTGGCTGGACCCCTGGCGGCTGATGCTAGAGCGAAGGAGAGAGCGGACGCGGGAGCTGACACGTGAACGGGAGCTGGAG

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	92.10%	0.60%	3.94%	3.39%	NA
All Indica	2759	92.60%	0.20%	2.21%	5.04%	NA
All Japonica	1512	91.30%	0.80%	7.67%	0.26%	NA
Aus	269	88.50%	4.50%	1.49%	5.58%	NA
Indica I	595	98.00%	0.00%	0.67%	1.34%	NA
Indica II	465	90.10%	0.00%	5.59%	4.30%	NA
Indica III	913	92.70%	0.20%	0.55%	6.57%	NA
Indica Intermediate	786	89.80%	0.40%	3.31%	6.49%	NA
Temperate Japonica	767	98.30%	0.10%	1.56%	0.00%	NA
Tropical Japonica	504	78.80%	2.00%	18.65%	0.60%	NA
Japonica Intermediate	241	95.00%	0.40%	4.15%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	0.00%	5.56%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1013317545	C -> T	LOC_Os10g25710.1	synonymous_variant ; p.Ser265Ser; LOW	synonymous_codon	Average:63.635; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg1013317545	C -> DEL	LOC_Os10g25710.1	N	frameshift_variant	Average:63.635; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013317545	4.39E-06	7.10E-08	mr1639	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