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Detailed information for vg1128141588:

Variant ID: vg1128141588 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28141588
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.03, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTCTGTATTGCCAAAAACGAACGAACTTGAAAACCGACTCAAACACGAATGATTTACCAAAATACCGGCAAAAACATCTTCAATTTTTATAATAGCAG[A/C]
GATAGAGATATAACAACTACTACACTAACATTATCTTCCCAACTAATCAAAATCCTTATAACCATTCAATTTACCCATCAATTTCCACTTCTCAACTAAC

Reverse complement sequence

GTTAGTTGAGAAGTGGAAATTGATGGGTAAATTGAATGGTTATAAGGATTTTGATTAGTTGGGAAGATAATGTTAGTGTAGTAGTTGTTATATCTCTATC[T/G]
CTGCTATTATAAAAATTGAAGATGTTTTTGCCGGTATTTTGGTAAATCATTCGTGTTTGAGTCGGTTTTCAAGTTCGTTCGTTTTTGGCAATACAGACAT

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	79.90%	7.80%	0.95%	11.34%	NA
All Indica	2759	86.40%	7.10%	1.20%	5.36%	NA
All Japonica	1512	73.30%	10.10%	0.60%	16.01%	NA
Aus	269	50.90%	5.20%	0.00%	43.87%	NA
Indica I	595	96.60%	2.00%	0.00%	1.34%	NA
Indica II	465	92.70%	2.20%	1.08%	4.09%	NA
Indica III	913	81.20%	11.60%	1.42%	5.81%	NA
Indica Intermediate	786	80.90%	8.50%	1.91%	8.65%	NA
Temperate Japonica	767	87.20%	8.00%	0.39%	4.43%	NA
Tropical Japonica	504	52.40%	16.10%	0.79%	30.75%	NA
Japonica Intermediate	241	73.00%	4.10%	0.83%	21.99%	NA
VI/Aromatic	96	82.30%	0.00%	0.00%	17.71%	NA
Intermediate	90	75.60%	8.90%	3.33%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128141588	A -> DEL	N	N	silent_mutation	Average:28.738; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N
vg1128141588	A -> C	LOC_Os11g46870.1	upstream_gene_variant ; 604.0bp to feature; MODIFIER	silent_mutation	Average:28.738; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N
vg1128141588	A -> C	LOC_Os11g46860-LOC_Os11g46870	intergenic_region ; MODIFIER	silent_mutation	Average:28.738; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128141588	NA	4.89E-07	mr1304	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
vg1128141588	1.83E-06	NA	mr1304_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