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Detailed information for vg0131782565:

Variant ID: vg0131782565 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 31782565
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

CATTCCACCCATGTGGTCGTACTTGTCTTATGTTCGGATGAAATTCCAAGGAAACGGTCCTTAAGTGCAAGAGCGGGAAACTGTACACCCGGTACGTTCC[C/T]
CGGTCCTCAGTTTTGGAAATTCATTTAGTTCGCAAGCACCGACCCAAGTGTCGGGTTTTCCAAGTCTTTTGTAAAACCCAAGTTTTACCCAAGATGTTTC

Reverse complement sequence

GAAACATCTTGGGTAAAACTTGGGTTTTACAAAAGACTTGGAAAACCCGACACTTGGGTCGGTGCTTGCGAACTAAATGAATTTCCAAAACTGAGGACCG[G/A]
GGAACGTACCGGGTGTACAGTTTCCCGCTCTTGCACTTAAGGACCGTTTCCTTGGAATTTCATCCGAACATAAGACAAGTACGACCACATGGGTGGAATG

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	38.90%	3.30%	25.48%	32.37%	NA
All Indica	2759	13.50%	5.50%	34.51%	46.43%	NA
All Japonica	1512	89.60%	0.00%	1.46%	8.93%	NA
Aus	269	16.00%	0.00%	74.35%	9.67%	NA
Indica I	595	22.70%	16.80%	31.43%	29.08%	NA
Indica II	465	13.50%	3.40%	35.05%	47.96%	NA
Indica III	913	5.50%	0.20%	34.06%	60.24%	NA
Indica Intermediate	786	15.90%	4.50%	37.02%	42.62%	NA
Temperate Japonica	767	99.50%	0.00%	0.26%	0.26%	NA
Tropical Japonica	504	71.60%	0.00%	3.37%	25.00%	NA
Japonica Intermediate	241	95.90%	0.00%	1.24%	2.90%	NA
VI/Aromatic	96	13.50%	0.00%	13.54%	72.92%	NA
Intermediate	90	60.00%	1.10%	18.89%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0131782565	C -> T	LOC_Os01g55220-LOC_Os01g55240	intergenic_region ; MODIFIER	silent_mutation	Average:26.533; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg0131782565	C -> DEL	N	N	silent_mutation	Average:26.533; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0131782565	5.57E-07	5.56E-07	mr1760_2	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
vg0131782565	1.54E-06	1.54E-06	mr1760_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