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Detailed information for vg1123023188:

Variant ID: vg1123023188 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23023188
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:

ACGGTTCGTGAAGGCTTCAAGGTACCGAGGGCCGAAAAACAGTTTGTGAAGGCTCCAAGGTGCGCTTCATTGAGAAGGGGATACATCTTTTCTTCTTTAT[C/A]
ATCCAAGAATTGGCACACTTCGACGACATCATCAAGACTTTGGAGATAGGCTAATATTTAGTTTGTGTTCTCATGTTTAGTTTACACTCCAAATGCAATA

Reverse complement sequence

TATTGCATTTGGAGTGTAAACTAAACATGAGAACACAAACTAAATATTAGCCTATCTCCAAAGTCTTGATGATGTCGTCGAAGTGTGCCAATTCTTGGAT[G/T]
ATAAAGAAGAAAAGATGTATCCCCTTCTCAATGAAGCGCACCTTGGAGCCTTCACAAACTGTTTTTCGGCCCTCGGTACCTTGAAGCCTTCACGAACCGT

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	93.10%	3.90%	0.13%	2.86%	NA
All Indica	2759	95.10%	1.30%	0.18%	3.44%	NA
All Japonica	1512	98.90%	0.90%	0.00%	0.20%	NA
Aus	269	40.10%	47.20%	0.37%	12.27%	NA
Indica I	595	99.20%	0.20%	0.17%	0.50%	NA
Indica II	465	98.70%	0.00%	0.00%	1.29%	NA
Indica III	913	88.40%	3.10%	0.22%	8.32%	NA
Indica Intermediate	786	97.60%	0.90%	0.25%	1.27%	NA
Temperate Japonica	767	99.00%	0.90%	0.00%	0.13%	NA
Tropical Japonica	504	98.80%	0.80%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	5.20%	0.00%	2.08%	NA
Intermediate	90	94.40%	3.30%	0.00%	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
vg1123023188	C -> A	LOC_Os11g38750-LOC_Os11g38760	intergenic_region ; MODIFIER	silent_mutation	Average:44.578; most accessible tissue: Zhenshan97 young leaf, score: 62.534	N	N	N	N
vg1123023188	C -> DEL	N	N	silent_mutation	Average:44.578; most accessible tissue: Zhenshan97 young leaf, score: 62.534	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123023188	NA	2.80E-08	mr1006	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
vg1123023188	NA	3.09E-07	mr1007	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
vg1123023188	NA	2.21E-08	mr1052	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
vg1123023188	NA	4.97E-08	mr1510_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