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Detailed information for vg0907583714:

Variant ID: vg0907583714 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7583714
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCGCCCAGCCGCTTGTCGTGTTAGCAACTGGCTATACTCGACGACCGACATATCGCCGATCATCCTACGGGCCTCGTTTTCAGCCTGGTCAAGGGTCAA[C/T]
GCTGCAAAAGTAAAGTGTGTAGCTATGTTAACAGTCAGACAAGGCAAGATAACAAAGCACAGCAGTGTATAGCAAGAGAACCGTCTTACTGTCCGTCCCC

Reverse complement sequence

GGGGACGGACAGTAAGACGGTTCTCTTGCTATACACTGCTGTGCTTTGTTATCTTGCCTTGTCTGACTGTTAACATAGCTACACACTTTACTTTTGCAGC[G/A]
TTGACCCTTGACCAGGCTGAAAACGAGGCCCGTAGGATGATCGGCGATATGTCGGTCGTCGAGTATAGCCAGTTGCTAACACGACAAGCGGCTGGGCGGG

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	51.80%	7.40%	15.21%	25.56%	NA
All Indica	2759	39.00%	1.70%	24.39%	34.94%	NA
All Japonica	1512	72.50%	19.60%	1.19%	6.75%	NA
Aus	269	43.10%	0.00%	8.55%	48.33%	NA
Indica I	595	55.80%	1.70%	9.08%	33.45%	NA
Indica II	465	44.50%	1.10%	33.12%	21.29%	NA
Indica III	913	20.50%	1.20%	30.67%	47.65%	NA
Indica Intermediate	786	44.50%	2.50%	23.54%	29.39%	NA
Temperate Japonica	767	78.70%	6.90%	2.09%	12.26%	NA
Tropical Japonica	504	76.20%	23.00%	0.20%	0.60%	NA
Japonica Intermediate	241	44.80%	52.70%	0.41%	2.07%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	73.30%	10.00%	4.44%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907583714	C -> DEL	LOC_Os09g13160.1	N	frameshift_variant	Average:10.48; most accessible tissue: Callus, score: 16.861	N	N	N	N
vg0907583714	C -> T	LOC_Os09g13160.1	splice_region_variant&synonymous_variant ; p.Thr157Thr; LOW	synonymous_codon	Average:10.48; most accessible tissue: Callus, score: 16.861	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907583714	2.14E-06	2.14E-06	mr1313_2	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