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Detailed information for vg0901839940:

Variant ID: vg0901839940 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1839940
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAACTAGGGATCGTGGGCTTGGTAGCTCGCTAGGATGAGCTCCACCGCGGCCCGCGCCAGGGAAGCCGACGACGACTTGAGGACCGTGTCAACCTCCCC[C/T]
TGCAACTTCTCCAGGTCGACCGCCATCTCGTCTAGCCAGTGTGCGAGCGCTGGACTAGTAGATGGTAACTTCTTGTCCCAGCACATCGAGATGCCCACCC

Reverse complement sequence

GGGTGGGCATCTCGATGTGCTGGGACAAGAAGTTACCATCTACTAGTCCAGCGCTCGCACACTGGCTAGACGAGATGGCGGTCGACCTGGAGAAGTTGCA[G/A]
GGGGAGGTTGACACGGTCCTCAAGTCGTCGTCGGCTTCCCTGGCGCGGGCCGCGGTGGAGCTCATCCTAGCGAGCTACCAAGCCCACGATCCCTAGTTCC

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	96.70%	2.30%	1.06%	0.00%	NA
All Indica	2759	94.50%	3.70%	1.81%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.80%	0.20%	1.01%	0.00%	NA
Indica II	465	81.70%	12.00%	6.24%	0.00%	NA
Indica III	913	98.60%	1.30%	0.11%	0.00%	NA
Indica Intermediate	786	94.00%	4.20%	1.78%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0901839940	C -> T	LOC_Os09g03660.1	synonymous_variant ; p.Gln746Gln; LOW	synonymous_codon	Average:74.122; most accessible tissue: Zhenshan97 young leaf, score: 87.584	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901839940	NA	5.83E-06	mr1319	Ind_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
vg0901839940	2.04E-06	2.04E-06	mr1848_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