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Detailed information for vg1005442522:

Variant ID: vg1005442522 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5442522
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.13, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCTCTGTCAACATTTACTAAAGCATGAATCACTTGGTCAATGGCTCCTTGAGTCAGTAGTGATTCTATCTCTTGGTTTCTGTCTGGACTAACATGTGA[T/C]
GGGGTCATCTTTTCTGTTCGTAAAAGCTGCAGTGTTATCTCTACTTGCCTCATTGTAGGCCTTTCTTCACCTTTTAGCTTTATGCACATCTCAGCAAGGG

Reverse complement sequence

CCCTTGCTGAGATGTGCATAAAGCTAAAAGGTGAAGAAAGGCCTACAATGAGGCAAGTAGAGATAACACTGCAGCTTTTACGAACAGAAAAGATGACCCC[A/G]
TCACATGTTAGTCCAGACAGAAACCAAGAGATAGAATCACTACTGACTCAAGGAGCCATTGACCAAGTGATTCATGCTTTAGTAAATGTTGACAGAGCTA

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	77.60%	22.40%	0.00%	0.00%	NA
All Indica	2759	98.50%	1.50%	0.00%	0.00%	NA
All Japonica	1512	38.60%	61.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	98.10%	1.90%	0.00%	0.00%	NA
Temperate Japonica	767	26.60%	73.40%	0.00%	0.00%	NA
Tropical Japonica	504	50.60%	49.40%	0.00%	0.00%	NA
Japonica Intermediate	241	51.50%	48.50%	0.00%	0.00%	NA
VI/Aromatic	96	46.90%	53.10%	0.00%	0.00%	NA
Intermediate	90	60.00%	40.00%	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
vg1005442522	T -> C	LOC_Os10g10030.1	synonymous_variant ; p.Pro861Pro; LOW	synonymous_codon	Average:53.38; most accessible tissue: Callus, score: 87.632	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005442522	4.20E-14	3.70E-27	mr1768	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
vg1005442522	4.83E-07	1.20E-10	mr1768	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
vg1005442522	1.73E-21	5.37E-46	mr1768_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
vg1005442522	1.04E-08	7.34E-12	mr1768_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