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Detailed information for vg0427974731:

Variant ID: vg0427974731 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27974731
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACATAAGACAAGTACGACCACATGGGTGGAATGGGACACCCCTGGCTGAGTAACTAGCTTATCAGGGGAGCCTTGATGCCGAGAGACATGTGGATTCGC[C/T]
GGGGTGGTGTCAGGGAGGACCCCTGGGCTTCCTGGCACAGTATGGTCTAGGACCTAACCTGTTGTTGGTCTGGGACCCCTCTCGTCGGCATATGGTAAAC

Reverse complement sequence

GTTTACCATATGCCGACGAGAGGGGTCCCAGACCAACAACAGGTTAGGTCCTAGACCATACTGTGCCAGGAAGCCCAGGGGTCCTCCCTGACACCACCCC[G/A]
GCGAATCCACATGTCTCTCGGCATCAAGGCTCCCCTGATAAGCTAGTTACTCAGCCAGGGGTGTCCCATTCCACCCATGTGGTCGTACTTGTCTTATGTT

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	54.70%	2.20%	18.07%	25.01%	NA
All Indica	2759	29.50%	0.10%	29.14%	41.28%	NA
All Japonica	1512	90.90%	6.40%	2.18%	0.46%	NA
Aus	269	89.60%	0.00%	1.86%	8.55%	NA
Indica I	595	25.20%	0.00%	18.99%	55.80%	NA
Indica II	465	13.30%	0.00%	41.29%	45.38%	NA
Indica III	913	36.80%	0.30%	30.01%	32.86%	NA
Indica Intermediate	786	33.70%	0.00%	28.63%	37.66%	NA
Temperate Japonica	767	98.30%	0.00%	1.43%	0.26%	NA
Tropical Japonica	504	77.40%	18.80%	2.98%	0.79%	NA
Japonica Intermediate	241	95.90%	0.80%	2.90%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	3.30%	13.33%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0427974731	C -> DEL	N	N	silent_mutation	Average:9.517; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0427974731	C -> T	LOC_Os04g47100.1	downstream_gene_variant ; 2955.0bp to feature; MODIFIER	silent_mutation	Average:9.517; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0427974731	C -> T	LOC_Os04g47100-LOC_Os04g47110	intergenic_region ; MODIFIER	silent_mutation	Average:9.517; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427974731	1.64E-06	1.64E-06	mr1526	Jap_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
vg0427974731	NA	5.82E-06	mr1211_2	Jap_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