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Detailed information for vg1122566432:

Variant ID: vg1122566432 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22566432
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: 313. )

Flanking Sequence (100 bp) in Reference Genome:

CTGATGTCGTAATGCAGAAGCTGAAAATGTACGAAGAAATGTTGCTGTTAGAAACTGGAAACAACTCAACATGTGTATGTGAGATATGGCAATACTATGA[C/A]
AGGAATACAGGCATACAGCTCCCACGTGTATGCGGAAAGTGCTAACATCTTTCATATGCTTGGTCAGTTACCATGTCTTGCGACAAAACGTTTGTCAAAC

Reverse complement sequence

GTTTGACAAACGTTTTGTCGCAAGACATGGTAACTGACCAAGCATATGAAAGATGTTAGCACTTTCCGCATACACGTGGGAGCTGTATGCCTGTATTCCT[G/T]
TCATAGTATTGCCATATCTCACATACACATGTTGAGTTGTTTCCAGTTTCTAACAGCAACATTTCTTCGTACATTTTCAGCTTCTGCATTACGACATCAG

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	95.00%	4.90%	0.02%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	86.40%	13.60%	0.07%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	78.10%	21.80%	0.13%	0.00%	NA
Tropical Japonica	504	94.80%	5.20%	0.00%	0.00%	NA
Japonica Intermediate	241	95.00%	5.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1122566432	C -> A	LOC_Os11g38030.1	upstream_gene_variant ; 1030.0bp to feature; MODIFIER	silent_mutation	Average:68.302; most accessible tissue: Callus, score: 90.34	N	N	N	N
vg1122566432	C -> A	LOC_Os11g38050.1	downstream_gene_variant ; 3549.0bp to feature; MODIFIER	silent_mutation	Average:68.302; most accessible tissue: Callus, score: 90.34	N	N	N	N
vg1122566432	C -> A	LOC_Os11g38040.1	intron_variant ; MODIFIER	silent_mutation	Average:68.302; most accessible tissue: Callus, score: 90.34	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122566432	8.61E-06	NA	mr1310	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
vg1122566432	1.61E-09	NA	mr1926	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
vg1122566432	5.49E-06	NA	mr1310_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