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Detailed information for vg1014833617:

Variant ID: vg1014833617 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14833617
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.14, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCGCAAACCGCCTTGACCGGTTGCTTCACTACCTGCCCGCCATCATTATATTTGGTGTTTTATTAATAGTTTTTAGATGGCCCATTAACCGCCACCAC[C/T]
CTACTCCTTTATAGGTCTATTACTTAATTAATCACGTCATGTGTTTTAGATGGTCTTTTCTTCCAATAGTCTTTATTTTTTTATCACCAATTTTAGTTAT

Reverse complement sequence

ATAACTAAAATTGGTGATAAAAAAATAAAGACTATTGGAAGAAAAGACCATCTAAAACACATGACGTGATTAATTAAGTAATAGACCTATAAAGGAGTAG[G/A]
GTGGTGGCGGTTAATGGGCCATCTAAAAACTATTAATAAAACACCAAATATAATGATGGCGGGCAGGTAGTGAAGCAACCGGTCAAGGCGGTTTGCGGGA

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	44.10%	25.10%	23.59%	7.22%	NA
All Indica	2759	10.90%	42.40%	34.87%	11.85%	NA
All Japonica	1512	99.40%	0.30%	0.20%	0.13%	NA
Aus	269	48.00%	1.10%	48.70%	2.23%	NA
Indica I	595	22.50%	32.60%	29.92%	14.96%	NA
Indica II	465	7.10%	32.00%	43.66%	17.20%	NA
Indica III	913	6.10%	57.10%	30.34%	6.46%	NA
Indica Intermediate	786	9.90%	38.80%	38.68%	12.60%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.40%	0.00%	NA
Japonica Intermediate	241	98.30%	0.40%	0.41%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	60.00%	12.20%	21.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1014833617	C -> T	LOC_Os10g28510.1	3_prime_UTR_variant ; 1572.0bp to feature; MODIFIER	silent_mutation	Average:28.675; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1014833617	C -> T	LOC_Os10g28510.2	3_prime_UTR_variant ; 1572.0bp to feature; MODIFIER	silent_mutation	Average:28.675; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1014833617	C -> DEL	N	N	silent_mutation	Average:28.675; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014833617	1.89E-06	1.17E-06	mr1646_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