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Detailed information for vg0327535213:

Variant ID: vg0327535213 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27535213
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

GTCGCCGGGAGATCTAGTCGAACCAACTCGATTACGATCTCGCCGGTTTCATCGAGTTCCATCGTTCCCTTTGTAACCTGTGGTTTTCCATCATATAATC[C/T]
CATATCAACTGAATTAGGGCTATTACCTATTAAGGGGCCTGAACCAGTATAATCCTCGTCTTTTGTTTGCTCGATGTCGTATTACGTAGATCCTTGTACC

Reverse complement sequence

GGTACAAGGATCTACGTAATACGACATCGAGCAAACAAAAGACGAGGATTATACTGGTTCAGGCCCCTTAATAGGTAATAGCCCTAATTCAGTTGATATG[G/A]
GATTATATGATGGAAAACCACAGGTTACAAAGGGAACGATGGAACTCGATGAAACCGGCGAGATCGTAATCGAGTTGGTTCGACTAGATCTCCCGGCGAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.40%	1.00%	1.57%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	92.40%	2.80%	4.76%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	86.60%	4.70%	8.74%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	95.40%	2.50%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	1.10%	2.22%	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
vg0327535213	C -> T	LOC_Os03g48364.1	missense_variant ; p.Pro115Leu; MODERATE	nonsynonymous_codon ; P115L	Average:56.425; most accessible tissue: Zhenshan97 flag leaf, score: 72.012	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327535213	1.92E-06	NA	mr1310	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
vg0327535213	2.20E-06	NA	mr1926	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