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Detailed information for vg0219809349:

Variant ID: vg0219809349 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 19809349
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, C: 0.16, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

TGGCCTAATTAGACTATCTTTGTTGCTGCCTTGTTCAAGTTTTAGTGATAATAATAAAGCTTTCGCTGTTTCATCTCATTCTGCTCGTACTGATAATTCT[T/C]
TGTGGCATAATCGTCTTTGTCATGTTAATTACAAATCTATATCTCGTATGATGTCACTAGATTTAATTCCCAAGCATGACACACGAGGTATAAAGTGTGA

Reverse complement sequence

TCACACTTTATACCTCGTGTGTCATGCTTGGGAATTAAATCTAGTGACATCATACGAGATATAGATTTGTAATTAACATGACAAAGACGATTATGCCACA[A/G]
AGAATTATCAGTACGAGCAGAATGAGATGAAACAGCGAAAGCTTTATTATTATCACTAAAACTTGAACAAGGCAGCAACAAAGATAGTCTAATTAGGCCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.20%	11.60%	7.15%	0.04%	NA
All Indica	2759	68.20%	19.80%	11.96%	0.07%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	97.80%	0.00%	2.23%	0.00%	NA
Indica I	595	92.40%	2.40%	5.21%	0.00%	NA
Indica II	465	63.70%	19.40%	16.77%	0.22%	NA
Indica III	913	53.10%	31.80%	15.12%	0.00%	NA
Indica Intermediate	786	70.00%	19.30%	10.56%	0.13%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	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	95.60%	3.30%	1.11%	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
vg0219809349	T -> DEL	N	N	silent_mutation	Average:21.91; most accessible tissue: Minghui63 flag leaf, score: 40.473	N	N	N	N
vg0219809349	T -> C	LOC_Os02g33340.1	intron_variant ; MODIFIER	silent_mutation	Average:21.91; most accessible tissue: Minghui63 flag leaf, score: 40.473	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0219809349	NA	4.18E-06	mr1074	Ind_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
vg0219809349	NA	3.96E-07	mr1098	Ind_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
vg0219809349	NA	2.40E-06	mr1130	Ind_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
vg0219809349	1.75E-06	NA	mr1184	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
vg0219809349	4.07E-06	4.07E-06	mr1184	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
vg0219809349	NA	5.25E-06	mr1311	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
vg0219809349	5.28E-06	1.10E-07	mr1387	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
vg0219809349	4.71E-06	4.71E-06	mr1387	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
vg0219809349	NA	2.85E-06	mr1520	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
vg0219809349	8.91E-06	NA	mr1589	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
vg0219809349	8.99E-06	3.41E-07	mr1589	Ind_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
vg0219809349	2.13E-06	2.12E-06	mr1694	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
vg0219809349	NA	9.79E-07	mr1497_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