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Detailed information for vg0713133131:

Variant ID: vg0713133131 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13133131
Reference Allele: C	Alternative Allele: A,T
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.02, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

CGACGCCTCCGACCCAAGAAGATGTGCGTGGGGGGCCGGATGCCCGCCTCAATATTGAGCGCCGACGCAATGGTCGTCGTGCTGCCCACGCAACGGAGTG[C/A,T]
GCTTCCTCGTCCGGAGCGCCACTTCAGTCTGGGCATGGGGGCCAGCCTCCCATGTCCCCGGTTGGCGGTGCCGGCTGTCGAGCCTTTGTGGCGAGCCTTC

Reverse complement sequence

GAAGGCTCGCCACAAAGGCTCGACAGCCGGCACCGCCAACCGGGGACATGGGAGGCTGGCCCCCATGCCCAGACTGAAGTGGCGCTCCGGACGAGGAAGC[G/T,A]
CACTCCGTTGCGTGGGCAGCACGACGACCATTGCGTCGGCGCTCAATATTGAGGCGGGCATCCGGCCCCCCACGCACATCTTCTTGGGTCGGAGGCGTCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.70%	42.20%	1.06%	7.09%	NA
All Indica	2759	81.50%	15.10%	0.91%	2.50%	NA
All Japonica	1512	1.50%	80.40%	1.19%	16.93%	NA
Aus	269	18.20%	81.80%	0.00%	0.00%	NA
Indica I	595	97.30%	2.50%	0.17%	0.00%	NA
Indica II	465	86.70%	11.20%	1.08%	1.08%	NA
Indica III	913	72.40%	21.90%	0.55%	5.15%	NA
Indica Intermediate	786	77.00%	19.10%	1.78%	2.16%	NA
Temperate Japonica	767	2.00%	68.80%	1.56%	27.64%	NA
Tropical Japonica	504	0.60%	96.00%	0.40%	2.98%	NA
Japonica Intermediate	241	1.70%	84.60%	1.66%	12.03%	NA
VI/Aromatic	96	2.10%	92.70%	2.08%	3.12%	NA
Intermediate	90	28.90%	57.80%	5.56%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713133131	C -> DEL	N	N	silent_mutation	Average:58.629; most accessible tissue: Zhenshan97 flag leaf, score: 78.761	N	N	N	N
vg0713133131	C -> A	LOC_Os07g23300.1	intron_variant ; MODIFIER	silent_mutation	Average:58.629; most accessible tissue: Zhenshan97 flag leaf, score: 78.761	N	N	N	N
vg0713133131	C -> T	LOC_Os07g23300.1	intron_variant ; MODIFIER	N	Average:58.629; most accessible tissue: Zhenshan97 flag leaf, score: 78.761	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713133131	NA	7.46E-06	mr1872	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
vg0713133131	5.04E-06	9.90E-07	mr1039_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
vg0713133131	NA	4.12E-06	mr1558_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
vg0713133131	1.95E-06	9.69E-08	mr1632_2	Jap_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