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Detailed information for vg0400844895:

Variant ID: vg0400844895 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 844895
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, T: 0.41, G: 0.01, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

ACGGCTGGGCTTGTAGTGTAGCTTTCCTCTAGCCGACGCATCCAGGCAAGGGTGGGCGTGATGGAGTTTGGATGGGCCCTGCGACGGCCTATGCGACTTC[T/C]
GGATTCACCTAGGCACGAGAGGGGACTGCCCGCTGCCTTGCGAGGAGTGGGGGTGAAACCTGAGGTGTGGTGTGCTTGGTTAGAGGGGGTTATGCGAAGG

Reverse complement sequence

CCTTCGCATAACCCCCTCTAACCAAGCACACCACACCTCAGGTTTCACCCCCACTCCTCGCAAGGCAGCGGGCAGTCCCCTCTCGTGCCTAGGTGAATCC[A/G]
GAAGTCGCATAGGCCGTCGCAGGGCCCATCCAAACTCCATCACGCCCACCCTTGCCTGGATGCGTCGGCTAGAGGAAAGCTACACTACAAGCCCAGCCGT

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	52.60%	31.50%	14.54%	1.44%	NA
All Indica	2759	65.30%	27.80%	6.31%	0.54%	NA
All Japonica	1512	22.20%	44.00%	30.42%	3.44%	NA
Aus	269	88.50%	7.40%	4.09%	0.00%	NA
Indica I	595	88.20%	10.30%	1.34%	0.17%	NA
Indica II	465	54.40%	31.80%	11.83%	1.94%	NA
Indica III	913	57.90%	35.80%	6.13%	0.11%	NA
Indica Intermediate	786	63.10%	29.40%	7.00%	0.51%	NA
Temperate Japonica	767	5.70%	77.60%	16.30%	0.39%	NA
Tropical Japonica	504	38.30%	4.40%	48.61%	8.73%	NA
Japonica Intermediate	241	40.70%	19.90%	37.34%	2.07%	NA
VI/Aromatic	96	66.70%	5.20%	28.12%	0.00%	NA
Intermediate	90	48.90%	33.30%	16.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400844895	T -> C	LOC_Os04g02360.1	downstream_gene_variant ; 2799.0bp to feature; MODIFIER	silent_mutation	Average:23.317; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N
vg0400844895	T -> C	LOC_Os04g02370.1	intron_variant ; MODIFIER	silent_mutation	Average:23.317; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N
vg0400844895	T -> DEL	N	N	silent_mutation	Average:23.317; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400844895	NA	5.19E-07	mr1443	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