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Detailed information for vg0208687924:

Variant ID: vg0208687924 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8687924
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCGGGGTGTTATGCATTACCTGTGATATAGTACCAGTCCCAGGATACACTAGCTGGTACACACAGATTAAATGTGGAATCAAATAAACTGCTTTATTA[C/T]
ATCACTGGGTAGTAGTCCTTACATAAGTTGCTATCATGGACAGACCCATAGATGAGCAACACAACATTACAGAAAACCATAAAAGCGACGGTGCAGAAGC

Reverse complement sequence

GCTTCTGCACCGTCGCTTTTATGGTTTTCTGTAATGTTGTGTTGCTCATCTATGGGTCTGTCCATGATAGCAACTTATGTAAGGACTACTACCCAGTGAT[G/A]
TAATAAAGCAGTTTATTTGATTCCACATTTAATCTGTGTGTACCAGCTAGTGTATCCTGGGACTGGTACTATATCACAGGTAATGCATAACACCCCGGTG

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	63.80%	8.10%	10.41%	17.73%	NA
All Indica	2759	65.20%	6.20%	12.79%	15.77%	NA
All Japonica	1512	69.40%	0.60%	6.94%	23.08%	NA
Aus	269	22.70%	62.80%	7.06%	7.43%	NA
Indica I	595	67.40%	1.30%	8.57%	22.69%	NA
Indica II	465	53.80%	10.80%	23.66%	11.83%	NA
Indica III	913	67.80%	5.70%	11.72%	14.79%	NA
Indica Intermediate	786	67.30%	7.90%	10.81%	13.99%	NA
Temperate Japonica	767	85.90%	0.00%	1.30%	12.78%	NA
Tropical Japonica	504	53.00%	1.40%	14.29%	31.35%	NA
Japonica Intermediate	241	51.00%	0.80%	9.54%	38.59%	NA
VI/Aromatic	96	46.90%	21.90%	4.17%	27.08%	NA
Intermediate	90	66.70%	12.20%	12.22%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208687924	C -> T	LOC_Os02g15500-LOC_Os02g15510	intergenic_region ; MODIFIER	silent_mutation	Average:31.378; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg0208687924	C -> DEL	N	N	silent_mutation	Average:31.378; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208687924	4.84E-07	NA	mr1224_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