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Detailed information for vg0510928675:

Variant ID: vg0510928675 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 10928675
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: 126. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAATCCCCTTGGATACACCTCCCACCCTGTATCCGGGCACACAAGCTGGAGTCGGGTGAGGATTCTTGCGACTCCAACACCTCCAACGCCAGCACCGC[C/T]
AAGGTTGCGACGACGATGTCCTAAATGCTGCCAATGCCCTAACCATGGTGTGCGCCAAATCTCCAGAAGCGGTCATCGATTTCGTTTGCCGAGTGAGCCC

Reverse complement sequence

GGGCTCACTCGGCAAACGAAATCGATGACCGCTTCTGGAGATTTGGCGCACACCATGGTTAGGGCATTGGCAGCATTTAGGACATCGTCGTCGCAACCTT[G/A]
GCGGTGCTGGCGTTGGAGGTGTTGGAGTCGCAAGAATCCTCACCCGACTCCAGCTTGTGTGCCCGGATACAGGGTGGGAGGTGTATCCAAGGGGATTGAA

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	82.90%	4.40%	2.67%	10.03%	NA
All Indica	2759	79.20%	6.80%	3.62%	10.44%	NA
All Japonica	1512	98.10%	0.90%	0.60%	0.33%	NA
Aus	269	29.40%	0.00%	4.83%	65.80%	NA
Indica I	595	73.10%	11.80%	7.90%	7.23%	NA
Indica II	465	83.40%	12.90%	2.15%	1.51%	NA
Indica III	913	80.60%	0.50%	2.08%	16.76%	NA
Indica Intermediate	786	79.50%	6.60%	3.05%	10.81%	NA
Temperate Japonica	767	97.50%	1.60%	0.91%	0.00%	NA
Tropical Japonica	504	98.80%	0.20%	0.20%	0.79%	NA
Japonica Intermediate	241	98.80%	0.40%	0.41%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	8.90%	4.44%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0510928675	C -> T	LOC_Os05g18810.1	intron_variant ; MODIFIER	silent_mutation	Average:60.892; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N
vg0510928675	C -> DEL	N	N	silent_mutation	Average:60.892; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0510928675	8.25E-07	4.53E-06	mr1651	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
vg0510928675	2.39E-06	2.39E-06	mr1651	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
vg0510928675	NA	1.32E-07	mr1707	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