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Detailed information for vg0314971782:

Variant ID: vg0314971782 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14971782
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCTTTGCCCGTCGGCGTGCCGCCGCGAGGCCGCCGGCCGCCGGCCGCCCGATGGGATGATGGAGGGGGAAGGAGAGGAGTTATAGGAGAAGTTAGAGAG[G/T]
AGGAAGAGGAAGGGATGATGGGGGAGGGAAGGAGAGGAGTTACAGGAGAGGAGGAGGAGGAAGATGAAGAGATGGGATGAAGAGATAAGGTCAGTGGAGG

Reverse complement sequence

CCTCCACTGACCTTATCTCTTCATCCCATCTCTTCATCTTCCTCCTCCTCCTCTCCTGTAACTCCTCTCCTTCCCTCCCCCATCATCCCTTCCTCTTCCT[C/A]
CTCTCTAACTTCTCCTATAACTCCTCTCCTTCCCCCTCCATCATCCCATCGGGCGGCCGGCGGCCGGCGGCCTCGCGGCGGCACGCCGACGGGCAAAGGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.20%	7.80%	1.48%	48.54%	NA
All Indica	2759	28.70%	0.00%	1.81%	69.52%	NA
All Japonica	1512	54.40%	23.90%	0.99%	20.77%	NA
Aus	269	98.90%	0.00%	0.00%	1.12%	NA
Indica I	595	49.90%	0.00%	0.50%	49.58%	NA
Indica II	465	42.20%	0.00%	1.08%	56.77%	NA
Indica III	913	14.10%	0.00%	3.61%	82.26%	NA
Indica Intermediate	786	21.50%	0.00%	1.15%	77.35%	NA
Temperate Japonica	767	51.20%	44.20%	1.04%	3.52%	NA
Tropical Japonica	504	51.40%	1.60%	1.19%	45.83%	NA
Japonica Intermediate	241	70.50%	5.80%	0.41%	23.24%	NA
VI/Aromatic	96	66.70%	0.00%	3.12%	30.21%	NA
Intermediate	90	57.80%	6.70%	2.22%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0314971782	G -> T	LOC_Os03g26130.1	downstream_gene_variant ; 3260.0bp to feature; MODIFIER	silent_mutation	Average:19.252; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N
vg0314971782	G -> T	LOC_Os03g26130-LOC_Os03g26180	intergenic_region ; MODIFIER	silent_mutation	Average:19.252; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N
vg0314971782	G -> DEL	N	N	silent_mutation	Average:19.252; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314971782	NA	6.62E-07	mr1521	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
vg0314971782	9.25E-08	9.25E-08	mr1955	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