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Detailed information for vg0804836535:

Variant ID: vg0804836535 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4836535
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTCGCTCGAGAAGCACATGGCGTTGGAAAAAGGCAAGCGAGTACGAGTGGTCGAGAAGGATGCGGAGGCGACTCCTCAGGAATCGGACTCAGCATATC[C/T]
AGACTCTGACCTCCACGTCTCGCACATTTTCGGAGGCTCCACAGTGTACTCCTCAAAGCAAGAATACAAGAAAGTGGAACATGAAGTCTGTTCGACATGG

Reverse complement sequence

CCATGTCGAACAGACTTCATGTTCCACTTTCTTGTATTCTTGCTTTGAGGAGTACACTGTGGAGCCTCCGAAAATGTGCGAGACGTGGAGGTCAGAGTCT[G/A]
GATATGCTGAGTCCGATTCCTGAGGAGTCGCCTCCGCATCCTTCTCGACCACTCGTACTCGCTTGCCTTTTTCCAACGCCATGTGCTTCTCGAGCGACTT

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	43.30%	4.10%	9.54%	43.04%	NA
All Indica	2759	22.10%	6.90%	11.09%	59.91%	NA
All Japonica	1512	88.20%	0.00%	0.46%	11.31%	NA
Aus	269	16.00%	1.10%	47.96%	34.94%	NA
Indica I	595	17.00%	3.40%	9.41%	70.25%	NA
Indica II	465	36.30%	8.80%	8.39%	46.45%	NA
Indica III	913	20.00%	7.70%	10.73%	61.56%	NA
Indica Intermediate	786	19.80%	7.60%	14.38%	58.14%	NA
Temperate Japonica	767	90.70%	0.00%	0.52%	8.74%	NA
Tropical Japonica	504	87.50%	0.00%	0.60%	11.90%	NA
Japonica Intermediate	241	81.70%	0.00%	0.00%	18.26%	NA
VI/Aromatic	96	9.40%	0.00%	4.17%	86.46%	NA
Intermediate	90	56.70%	1.10%	5.56%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804836535	C -> T	LOC_Os08g08390.1	stop_gained ; p.Gln393*; HIGH	stop_gained	Average:8.12; most accessible tissue: Minghui63 young leaf, score: 15.967	N	N	N	N
vg0804836535	C -> DEL	LOC_Os08g08390.1	N	frameshift_variant	Average:8.12; most accessible tissue: Minghui63 young leaf, score: 15.967	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804836535	2.13E-07	2.13E-07	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