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Detailed information for vg1011143314:

Variant ID: vg1011143314 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11143314
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGCCTCCGTCGCCGCCGACTGGTGTCCTCGCCTATACGGTTCGTTGGTCACACCACTGTTCATGGGCGTCTACGTCTTCACCGACCGGCTTGCCTTCGC[C/T]
GCCGCCGACTGGTGTCTTCGCCTGCACGGCTGACCTATTATGTCGCCGTTTGTTGGGCGTCTACGCTTTCACCGATCGGCTTGCCTTCGCCGCCGCTGAC

Reverse complement sequence

GTCAGCGGCGGCGAAGGCAAGCCGATCGGTGAAAGCGTAGACGCCCAACAAACGGCGACATAATAGGTCAGCCGTGCAGGCGAAGACACCAGTCGGCGGC[G/A]
GCGAAGGCAAGCCGGTCGGTGAAGACGTAGACGCCCATGAACAGTGGTGTGACCAACGAACCGTATAGGCGAGGACACCAGTCGGCGGCGACGGAGGCAG

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	91.30%	2.20%	0.59%	5.92%	NA
All Indica	2759	97.90%	0.10%	0.33%	1.67%	NA
All Japonica	1512	92.80%	6.60%	0.26%	0.33%	NA
Aus	269	33.50%	0.00%	4.09%	62.45%	NA
Indica I	595	98.30%	0.20%	0.00%	1.51%	NA
Indica II	465	99.60%	0.00%	0.00%	0.43%	NA
Indica III	913	97.90%	0.10%	0.55%	1.42%	NA
Indica Intermediate	786	96.60%	0.10%	0.51%	2.80%	NA
Temperate Japonica	767	91.00%	8.70%	0.26%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.20%	0.00%	NA
Japonica Intermediate	241	85.90%	11.60%	0.41%	2.07%	NA
VI/Aromatic	96	42.70%	0.00%	4.17%	53.12%	NA
Intermediate	90	88.90%	0.00%	0.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011143314	C -> T	LOC_Os10g21720.1	downstream_gene_variant ; 3747.0bp to feature; MODIFIER	silent_mutation	Average:65.434; most accessible tissue: Zhenshan97 flag leaf, score: 82.17	N	N	N	N
vg1011143314	C -> T	LOC_Os10g21700-LOC_Os10g21720	intergenic_region ; MODIFIER	silent_mutation	Average:65.434; most accessible tissue: Zhenshan97 flag leaf, score: 82.17	N	N	N	N
vg1011143314	C -> DEL	N	N	silent_mutation	Average:65.434; most accessible tissue: Zhenshan97 flag leaf, score: 82.17	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011143314	1.18E-06	1.18E-06	mr1566	Jap_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