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Detailed information for vg1205550390:

Variant ID: vg1205550390 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5550390
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAATAACTTATAAACCGCTAACCTTAACCTTAATTATAGCATCAATGGACCTATTGACTCACAACCAACTTAATTATATCTCTCGACATATATGCGGAT[G/T]
CTATTTACTTAATTCCAATGCCCTGATAAAAATATATGATCTTCTTTTAAGGATAAATGTACGATCTTATGCTGTGTTCGGCGCTGAGGGTTGGGAAACC

Reverse complement sequence

GGTTTCCCAACCCTCAGCGCCGAACACAGCATAAGATCGTACATTTATCCTTAAAAGAAGATCATATATTTTTATCAGGGCATTGGAATTAAGTAAATAG[C/A]
ATCCGCATATATGTCGAGAGATATAATTAAGTTGGTTGTGAGTCAATAGGTCCATTGATGCTATAATTAAGGTTAAGGTTAGCGGTTTATAAGTTATTTT

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	73.30%	6.80%	3.94%	15.98%	NA
All Indica	2759	55.00%	11.60%	6.71%	26.71%	NA
All Japonica	1512	99.40%	0.00%	0.00%	0.60%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	63.50%	4.20%	7.23%	25.04%	NA
Indica II	465	60.90%	3.20%	0.86%	35.05%	NA
Indica III	913	40.10%	24.00%	10.51%	25.41%	NA
Indica Intermediate	786	62.30%	7.80%	5.34%	24.55%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	98.40%	0.00%	0.00%	1.59%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	2.20%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205550390	G -> DEL	N	N	silent_mutation	Average:18.16; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1205550390	G -> T	LOC_Os12g10470.1	intron_variant ; MODIFIER	silent_mutation	Average:18.16; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205550390	2.38E-06	NA	mr1784	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