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Detailed information for vg1016225510:

Variant ID: vg1016225510 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 16225510
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCTAGCTCCACCAGCCATTTCTCCCCCCCATCTCCTCTCTGCTTGCGAGCTTGTCAACCGCGCAAAGGTTCATATATACACCGATCGAAATCGATCGG[T/A]
GTAGAGCCACACTCTTGGAGTCGATCGTTCGCTGGTTAGCTAACTAAGCTAAGCTGAGCTGCCTTGCTCTCTTCGACGATCAGGTTGCTTGGTTTGACGA

Reverse complement sequence

TCGTCAAACCAAGCAACCTGATCGTCGAAGAGAGCAAGGCAGCTCAGCTTAGCTTAGTTAGCTAACCAGCGAACGATCGACTCCAAGAGTGTGGCTCTAC[A/T]
CCGATCGATTTCGATCGGTGTATATATGAACCTTTGCGCGGTTGACAAGCTCGCAAGCAGAGAGGAGATGGGGGGGAGAAATGGCTGGTGGAGCTAGAGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.20%	5.50%	0.02%	0.34%	NA
All Indica	2759	99.20%	0.20%	0.00%	0.58%	NA
All Japonica	1512	86.30%	13.60%	0.07%	0.00%	NA
Aus	269	85.50%	14.50%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.20%	0.00%	0.00%	1.75%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	90.50%	9.40%	0.13%	0.00%	NA
Tropical Japonica	504	94.40%	5.60%	0.00%	0.00%	NA
Japonica Intermediate	241	56.00%	44.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg1016225510	T -> A	LOC_Os10g31040.1	5_prime_UTR_variant ; 10150.0bp to feature; MODIFIER	silent_mutation	Average:79.087; most accessible tissue: Callus, score: 95.414	N	N	N	N
vg1016225510	T -> A	LOC_Os10g31040.5	5_prime_UTR_variant ; 10150.0bp to feature; MODIFIER	silent_mutation	Average:79.087; most accessible tissue: Callus, score: 95.414	N	N	N	N
vg1016225510	T -> DEL	N	N	silent_mutation	Average:79.087; most accessible tissue: Callus, score: 95.414	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1016225510	8.86E-06	NA	mr1117	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
vg1016225510	NA	4.09E-06	mr1117	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
vg1016225510	4.84E-06	NA	mr1119	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
vg1016225510	6.11E-06	NA	mr1123	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
vg1016225510	NA	2.61E-06	mr1123	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
vg1016225510	1.17E-06	NA	mr1496	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
vg1016225510	NA	8.19E-06	mr1961	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
vg1016225510	1.13E-06	NA	mr1113_2	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
vg1016225510	NA	2.17E-06	mr1113_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
vg1016225510	4.99E-06	NA	mr1119_2	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
vg1016225510	NA	4.77E-06	mr1119_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
vg1016225510	1.25E-06	NA	mr1240_2	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
vg1016225510	NA	2.37E-06	mr1240_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
vg1016225510	1.29E-06	NA	mr1496_2	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
vg1016225510	NA	1.47E-06	mr1496_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
vg1016225510	5.37E-07	NA	mr1961_2	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
vg1016225510	NA	2.22E-06	mr1961_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