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Detailed information for vg1022900912:

Variant ID: vg1022900912 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 22900912
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGCGGTCTGCATCGACAGATTCACATTAATAAGTCAGCATATGGAGGATAATGGATTTTGAGGTATTGATTGTTGATACCTTCAACTTCCTTTGAAGC[C/T]
AGGTCTCTTTGTCTTGCCAGCTCTGCCTTGTTATTTTCCAGAATTTAGATCTGCTTCTCTAGTTGAGATATCTTGGCAGCTTGCACTACATTAACTTCGG

Reverse complement sequence

CCGAAGTTAATGTAGTGCAAGCTGCCAAGATATCTCAACTAGAGAAGCAGATCTAAATTCTGGAAAATAACAAGGCAGAGCTGGCAAGACAAAGAGACCT[G/A]
GCTTCAAAGGAAGTTGAAGGTATCAACAATCAATACCTCAAAATCCATTATCCTCCATATGCTGACTTATTAATGTGAATCTGTCGATGCAGACCGCAAG

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	44.10%	6.70%	46.42%	2.79%	NA
All Indica	2759	15.60%	10.90%	69.59%	3.91%	NA
All Japonica	1512	95.80%	0.30%	3.77%	0.07%	NA
Aus	269	24.20%	1.10%	67.29%	7.43%	NA
Indica I	595	36.80%	3.00%	55.29%	4.87%	NA
Indica II	465	7.70%	27.50%	60.43%	4.30%	NA
Indica III	913	7.70%	6.40%	82.80%	3.18%	NA
Indica Intermediate	786	13.50%	12.20%	70.48%	3.82%	NA
Temperate Japonica	767	99.20%	0.50%	0.26%	0.00%	NA
Tropical Japonica	504	89.10%	0.20%	10.52%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	88.50%	2.10%	8.33%	1.04%	NA
Intermediate	90	57.80%	8.90%	31.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1022900912	C -> T	LOC_Os10g42470.1	downstream_gene_variant ; 873.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1022900912	C -> T	LOC_Os10g42480.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1022900912	C -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1022900912	3.12E-06	3.10E-06	mr1258	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
vg1022900912	NA	1.08E-06	mr1979	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