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Detailed information for vg1003260501:

Variant ID: vg1003260501 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3260501
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

TACTCGTAAGGATTTCATGGTGTATTGTGACGCTTCGCGCCAAGGACTGAGGTGCGTGCTCATGCAGGAAGGACATGTGGTAGCCTATGCCTCACGCCAG[T/C]
TACGGCCCCATGAAGGCAACTACCCTACCCATGATTTGGAGTTAGCCGCGGTGGTTCATGCTCTAAAAATCTGGCGGCACTATCTCATTGGGAATCGCTG

Reverse complement sequence

CAGCGATTCCCAATGAGATAGTGCCGCCAGATTTTTAGAGCATGAACCACCGCGGCTAACTCCAAATCATGGGTAGGGTAGTTGCCTTCATGGGGCCGTA[A/G]
CTGGCGTGAGGCATAGGCTACCACATGTCCTTCCTGCATGAGCACGCACCTCAGTCCTTGGCGCGAAGCGTCACAATACACCATGAAATCCTTACGAGTA

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	56.40%	2.10%	14.58%	26.96%	NA
All Indica	2759	48.80%	2.90%	18.99%	29.25%	NA
All Japonica	1512	78.00%	0.60%	3.90%	17.53%	NA
Aus	269	12.60%	1.10%	20.45%	65.80%	NA
Indica I	595	66.10%	0.30%	6.55%	27.06%	NA
Indica II	465	47.30%	0.90%	17.85%	33.98%	NA
Indica III	913	35.70%	6.40%	30.56%	27.38%	NA
Indica Intermediate	786	51.90%	2.20%	15.65%	30.28%	NA
Temperate Japonica	767	70.40%	0.30%	3.26%	26.08%	NA
Tropical Japonica	504	89.90%	1.40%	3.37%	5.36%	NA
Japonica Intermediate	241	77.20%	0.00%	7.05%	15.77%	NA
VI/Aromatic	96	53.10%	5.20%	37.50%	4.17%	NA
Intermediate	90	58.90%	1.10%	16.67%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003260501	T -> C	LOC_Os10g06330.1	synonymous_variant ; p.Leu821Leu; LOW	synonymous_codon	Average:9.297; most accessible tissue: Callus, score: 32.732	N	N	N	N
vg1003260501	T -> DEL	LOC_Os10g06330.1	N	frameshift_variant	Average:9.297; most accessible tissue: Callus, score: 32.732	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003260501	7.81E-06	1.49E-07	mr1133_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1003260501	4.19E-06	6.47E-08	mr1667_2	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