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Detailed information for vg0116965632:

Variant ID: vg0116965632 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 16965632
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TGCATCTTTTGCACAGAACGAGATTCTTTTCTTGGATATGTTGTTACTCCACAGGGAATTGAGGTGGATGAGTCGAAAATTGAAGCCATAAAGAGTTGGC[C/T]
GGTTCCCTAAACCATCACACAGGTGAGGAGTTTTCTTGGTCTTGCAGGATTCTATCGCCGTTTCGTCAAAGATTTCAGTACCTTTGCTGCACCATTGAAT

Reverse complement sequence

ATTCAATGGTGCAGCAAAGGTACTGAAATCTTTGACGAAACGGCGATAGAATCCTGCAAGACCAAGAAAACTCCTCACCTGTGTGATGGTTTAGGGAACC[G/A]
GCCAACTCTTTATGGCTTCAATTTTCGACTCATCCACCTCAATTCCCTGTGGAGTAACAACATATCCAAGAAAAGAATCTCGTTCTGTGCAAAAGATGCA

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	41.70%	8.10%	9.14%	41.09%	NA
All Indica	2759	9.10%	11.80%	14.72%	64.44%	NA
All Japonica	1512	97.60%	0.00%	0.13%	2.31%	NA
Aus	269	36.80%	19.00%	7.06%	37.17%	NA
Indica I	595	10.40%	11.60%	14.79%	63.19%	NA
Indica II	465	12.00%	1.70%	20.86%	65.38%	NA
Indica III	913	4.50%	17.20%	11.72%	66.59%	NA
Indica Intermediate	786	11.60%	11.60%	14.50%	62.34%	NA
Temperate Japonica	767	99.20%	0.00%	0.13%	0.65%	NA
Tropical Japonica	504	94.80%	0.00%	0.20%	4.96%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	93.80%	0.00%	2.08%	4.17%	NA
Intermediate	90	61.10%	7.80%	3.33%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0116965632	C -> T	LOC_Os01g31020.1	intron_variant ; MODIFIER	silent_mutation	Average:9.959; most accessible tissue: Callus, score: 32.153	N	N	N	N
vg0116965632	C -> DEL	N	N	silent_mutation	Average:9.959; most accessible tissue: Callus, score: 32.153	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0116965632	2.79E-06	2.47E-06	mr1946	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