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Detailed information for vg1209004590:

Variant ID: vg1209004590 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9004590
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.80, C: 0.20, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

GACGAGGCGGCCGGTCAGTGAAGACGATGATGTCCATCAGCAGCGGCGCAATATGCCAGCCGTGAAGGCGAAGAGGCTTGTCGACGGAAGATGAGGCAGC[T/C]
GGCAGTGTAGAATATGTCATTATCAGCCATGGCGATAAAGACAACATGTTTGGATAAATCCAATACACGGTATGGTAGGCGGAGCCTGCAGCTTGATTAA

Reverse complement sequence

TTAATCAAGCTGCAGGCTCCGCCTACCATACCGTGTATTGGATTTATCCAAACATGTTGTCTTTATCGCCATGGCTGATAATGACATATTCTACACTGCC[A/G]
GCTGCCTCATCTTCCGTCGACAAGCCTCTTCGCCTTCACGGCTGGCATATTGCGCCGCTGCTGATGGACATCATCGTCTTCACTGACCGGCCGCCTCGTC

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	39.80%	37.90%	0.55%	21.71%	NA
All Indica	2759	54.20%	10.10%	0.94%	34.80%	NA
All Japonica	1512	4.40%	94.50%	0.00%	1.06%	NA
Aus	269	81.00%	5.20%	0.00%	13.75%	NA
Indica I	595	36.30%	20.80%	1.34%	41.51%	NA
Indica II	465	51.80%	12.00%	0.86%	35.27%	NA
Indica III	913	65.30%	2.30%	0.44%	31.98%	NA
Indica Intermediate	786	56.10%	9.90%	1.27%	32.70%	NA
Temperate Japonica	767	6.00%	93.00%	0.00%	1.04%	NA
Tropical Japonica	504	3.60%	95.60%	0.00%	0.79%	NA
Japonica Intermediate	241	1.20%	97.10%	0.00%	1.66%	NA
VI/Aromatic	96	72.90%	22.90%	0.00%	4.17%	NA
Intermediate	90	36.70%	53.30%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209004590	T -> C	LOC_Os12g15770.1	synonymous_variant ; p.Pro16Pro; LOW	synonymous_codon	Average:46.847; most accessible tissue: Minghui63 flag leaf, score: 77.828	N	N	N	N
vg1209004590	T -> DEL	LOC_Os12g15770.1	N	frameshift_variant	Average:46.847; most accessible tissue: Minghui63 flag leaf, score: 77.828	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209004590	NA	3.61E-08	mr1425	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
vg1209004590	NA	2.84E-06	mr1425	Ind_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
vg1209004590	NA	9.45E-06	mr1864_2	Ind_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