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Detailed information for vg0401888324:

Variant ID: vg0401888324 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1888324
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GTTCTCGAGGGACAAGGCTCTTGGACCTTTGAACTGCCTCGGTTGAACAAGTACTGATCCTAGCCCCCAGCCGTGAAGTTGGAAAGTTAATTTCCGATTA[C/T]
GCGGCTTGGTTAATACGCACGGGGAGAACTCTTACACGACCACGGCTGACATGGTCTTTCGTCTCTAAAGAATCCGACAAGGCCTTATCGGCTCCGGGCA

Reverse complement sequence

TGCCCGGAGCCGATAAGGCCTTGTCGGATTCTTTAGAGACGAAAGACCATGTCAGCCGTGGTCGTGTAAGAGTTCTCCCCGTGCGTATTAACCAAGCCGC[G/A]
TAATCGGAAATTAACTTTCCAACTTCACGGCTGGGGGCTAGGATCAGTACTTGTTCAACCGAGGCAGTTCAAAGGTCCAAGAGCCTTGTCCCTCGAGAAC

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	83.00%	15.50%	0.19%	1.31%	NA
All Indica	2759	98.40%	1.40%	0.07%	0.14%	NA
All Japonica	1512	54.60%	41.10%	0.46%	3.84%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	97.50%	2.40%	0.11%	0.00%	NA
Indica Intermediate	786	97.60%	1.80%	0.13%	0.51%	NA
Temperate Japonica	767	53.80%	37.70%	0.91%	7.56%	NA
Tropical Japonica	504	53.00%	47.00%	0.00%	0.00%	NA
Japonica Intermediate	241	60.60%	39.40%	0.00%	0.00%	NA
VI/Aromatic	96	55.20%	44.80%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0401888324	C -> DEL	N	N	silent_mutation	Average:49.274; most accessible tissue: Minghui63 flag leaf, score: 67.635	N	N	N	N
vg0401888324	C -> T	LOC_Os04g04080.1	downstream_gene_variant ; 3606.0bp to feature; MODIFIER	silent_mutation	Average:49.274; most accessible tissue: Minghui63 flag leaf, score: 67.635	N	N	N	N
vg0401888324	C -> T	LOC_Os04g04080-LOC_Os04g04100	intergenic_region ; MODIFIER	silent_mutation	Average:49.274; most accessible tissue: Minghui63 flag leaf, score: 67.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401888324	NA	9.78E-19	Awn_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0401888324	3.02E-06	NA	mr1670	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