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Detailed information for vg0102964097:

Variant ID: vg0102964097 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2964097
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:

ATCACACTGAACCTTCGGATTGGAGTACAGCGTCAGCCAAGACTGCGAGCTGTCCAGCCAAACCTGCTGCTTGTTCCGGCCATCGACGTCGATGAAGTTG[C/A]
GTGTCACCACAGCTTCATTTGACACATTGAACTGGAGATATTCCTCTCTGCTGTTGTCGAAGAACCCAAGGTGAAAGCCAGGTGAATTGCCGATCAGCTC

Reverse complement sequence

GAGCTGATCGGCAATTCACCTGGCTTTCACCTTGGGTTCTTCGACAACAGCAGAGAGGAATATCTCCAGTTCAATGTGTCAAATGAAGCTGTGGTGACAC[G/T]
CAACTTCATCGACGTCGATGGCCGGAACAAGCAGCAGGTTTGGCTGGACAGCTCGCAGTCTTGGCTGACGCTGTACTCCAATCCGAAGGTTCAGTGTGAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.40%	6.40%	1.21%	0.00%	NA
All Indica	2759	99.30%	0.70%	0.00%	0.00%	NA
All Japonica	1512	77.60%	18.60%	3.77%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.50%	1.50%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	62.70%	30.10%	7.17%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	80.90%	18.30%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0102964097	C -> A	LOC_Os01g06240.1	missense_variant ; p.Arg274Leu; MODERATE	nonsynonymous_codon ; R274L	Average:74.404; most accessible tissue: Zhenshan97 flag leaf, score: 82.17	possibly damaging	1.696	TOLERATED	0.50

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102964097	NA	2.28E-14	Heading_date	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0102964097	NA	6.17E-15	Spikelet_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0102964097	3.19E-06	NA	mr1092	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
vg0102964097	NA	1.19E-07	mr1092	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
vg0102964097	NA	2.31E-06	mr1354	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
vg0102964097	4.79E-06	NA	mr1889	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
vg0102964097	7.82E-08	NA	mr1354_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
vg0102964097	4.81E-07	3.75E-08	mr1354_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
vg0102964097	1.05E-06	NA	mr1902_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
vg0102964097	NA	1.94E-07	mr1902_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
vg0102964097	8.76E-06	8.76E-06	mr1958_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