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Detailed information for vg1003300020:

Variant ID: vg1003300020 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3300020
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

GTGGTCCGGAATACATTCCAAAAACAGAAGTAGGTAAGGCAGCGGAGTTAAGGCAGCGGCACGCCATTGCCACAGGCAACGACCGTAACTAAGACCTACT[G/T]
AGCGCCATCGTCTTCATCACCATCCTGGTAGTAAGCATAGGGATCCTCCGAAGCTTCATCTCCGACCACTGATTAAGTTTGTATATTGCAAGGGTGAGTA

Reverse complement sequence

TACTCACCCTTGCAATATACAAACTTAATCAGTGGTCGGAGATGAAGCTTCGGAGGATCCCTATGCTTACTACCAGGATGGTGATGAAGACGATGGCGCT[C/A]
AGTAGGTCTTAGTTACGGTCGTTGCCTGTGGCAATGGCGTGCCGCTGCCTTAACTCCGCTGCCTTACCTACTTCTGTTTTTGGAATGTATTCCGGACCAC

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	46.40%	11.20%	2.20%	40.25%	NA
All Indica	2759	22.50%	10.10%	3.66%	63.75%	NA
All Japonica	1512	96.20%	0.60%	0.07%	3.11%	NA
Aus	269	6.30%	83.30%	0.00%	10.41%	NA
Indica I	595	42.50%	2.00%	2.52%	52.94%	NA
Indica II	465	14.60%	29.20%	3.87%	52.26%	NA
Indica III	913	14.00%	4.80%	4.16%	77.00%	NA
Indica Intermediate	786	21.90%	10.90%	3.82%	63.36%	NA
Temperate Japonica	767	99.20%	0.10%	0.00%	0.65%	NA
Tropical Japonica	504	90.50%	1.20%	0.20%	8.13%	NA
Japonica Intermediate	241	98.80%	0.80%	0.00%	0.41%	NA
VI/Aromatic	96	52.10%	3.10%	0.00%	44.79%	NA
Intermediate	90	54.40%	15.60%	2.22%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003300020	G -> T	LOC_Os10g06410.1	upstream_gene_variant ; 3459.0bp to feature; MODIFIER	silent_mutation	Average:9.403; most accessible tissue: Callus, score: 42.841	N	N	N	N
vg1003300020	G -> T	LOC_Os10g06420.1	upstream_gene_variant ; 360.0bp to feature; MODIFIER	silent_mutation	Average:9.403; most accessible tissue: Callus, score: 42.841	N	N	N	N
vg1003300020	G -> T	LOC_Os10g06430.1	downstream_gene_variant ; 770.0bp to feature; MODIFIER	silent_mutation	Average:9.403; most accessible tissue: Callus, score: 42.841	N	N	N	N
vg1003300020	G -> T	LOC_Os10g06420-LOC_Os10g06430	intergenic_region ; MODIFIER	silent_mutation	Average:9.403; most accessible tissue: Callus, score: 42.841	N	N	N	N
vg1003300020	G -> DEL	N	N	silent_mutation	Average:9.403; most accessible tissue: Callus, score: 42.841	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003300020	9.67E-07	NA	mr1410	Ind_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