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Detailed information for vg0900240306:

Variant ID: vg0900240306 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 240306
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAGGGAGCTTGCTTTTGAAGCAGGGGATTATGTGTATCTCCATGTCACTCCGCTCAGGGGAGTACACCATTTCCAAACCAAAGGAAAGTTGGCACCACG[C/T]
TTTGTGGGACCATATTGGATTTTGGAACGCAGGGGTGAAGTTGCTTACCAGCTTGAGCTTCCCTCCAACATGCTTGGCATCCATGATGTGTTCCACGTCT

Reverse complement sequence

AGACGTGGAACACATCATGGATGCCAAGCATGTTGGAGGGAAGCTCAAGCTGGTAAGCAACTTCACCCCTGCGTTCCAAAATCCAATATGGTCCCACAAA[G/A]
CGTGGTGCCAACTTTCCTTTGGTTTGGAAATGGTGTACTCCCCTGAGCGGAGTGACATGGAGATACACATAATCCCCTGCTTCAAAAGCAAGCTCCCTTC

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	71.40%	0.60%	4.34%	23.64%	NA
All Indica	2759	61.30%	0.80%	2.10%	35.81%	NA
All Japonica	1512	89.90%	0.10%	9.52%	0.53%	NA
Aus	269	57.60%	1.50%	1.12%	39.78%	NA
Indica I	595	50.10%	0.70%	3.87%	45.38%	NA
Indica II	465	57.60%	1.10%	1.29%	40.00%	NA
Indica III	913	72.50%	0.70%	1.53%	25.30%	NA
Indica Intermediate	786	59.00%	0.80%	1.91%	38.30%	NA
Temperate Japonica	767	81.10%	0.10%	17.99%	0.78%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	97.10%	0.00%	2.49%	0.41%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	84.40%	2.20%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900240306	C -> DEL	LOC_Os09g01280.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900240306	C -> T	LOC_Os09g01280.1	synonymous_variant ; p.Arg440Arg; LOW	synonymous_codon	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900240306	8.11E-06	1.04E-06	mr1448	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
vg0900240306	4.88E-07	1.77E-06	mr1341_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