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Detailed information for vg1200003632:

Variant ID: vg1200003632 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3632
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

TTAACTATGACAGGAGTGGAAGATCCAAGGTTCCAAACCCCACCTTTCTTTTTTCTTTTACTTAATATGTGTCACTCTTTTTATGTTAAAATGCTCATTA[C/T]
TCATACCCTGTTTTGCCAGGGAACTGCAGAGGTTGTATTTTCCAGAAAATCTGACGCCCTGGCTGCTGTTAAGAGGTACAACAATGTGCAGCTGGATGGC

Reverse complement sequence

GCCATCCAGCTGCACATTGTTGTACCTCTTAACAGCAGCCAGGGCGTCAGATTTTCTGGAAAATACAACCTCTGCAGTTCCCTGGCAAAACAGGGTATGA[G/A]
TAATGAGCATTTTAACATAAAAAGAGTGACACATATTAAGTAAAAGAAAAAAGAAAGGTGGGGTTTGGAACCTTGGATCTTCCACTCCTGTCATAGTTAA

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	81.40%	0.10%	1.82%	16.74%	NA
All Indica	2759	90.00%	0.00%	1.45%	8.55%	NA
All Japonica	1512	63.60%	0.10%	2.84%	33.47%	NA
Aus	269	98.50%	0.00%	0.00%	1.49%	NA
Indica I	595	97.30%	0.00%	0.00%	2.69%	NA
Indica II	465	64.10%	0.20%	6.45%	29.25%	NA
Indica III	913	95.90%	0.00%	0.44%	3.61%	NA
Indica Intermediate	786	92.70%	0.00%	0.76%	6.49%	NA
Temperate Japonica	767	81.40%	0.00%	1.96%	16.69%	NA
Tropical Japonica	504	34.30%	0.40%	4.37%	60.91%	NA
Japonica Intermediate	241	68.00%	0.00%	2.49%	29.46%	NA
VI/Aromatic	96	66.70%	0.00%	2.08%	31.25%	NA
Intermediate	90	82.20%	0.00%	1.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1200003632	C -> DEL	N	N	silent_mutation	Average:32.599; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1200003632	C -> T	LOC_Os12g01020.1	downstream_gene_variant ; 1845.0bp to feature; MODIFIER	silent_mutation	Average:32.599; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1200003632	C -> T	LOC_Os12g01010.1	intron_variant ; MODIFIER	silent_mutation	Average:32.599; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200003632	NA	1.71E-14	mr1889	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
vg1200003632	NA	2.81E-11	mr1896	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
vg1200003632	NA	6.33E-13	mr1903	Ind_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
vg1200003632	NA	5.31E-17	mr1907	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
vg1200003632	6.76E-06	NA	mr1934	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
vg1200003632	NA	2.24E-14	mr1934	Ind_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
vg1200003632	NA	8.49E-13	mr1935	Ind_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
vg1200003632	NA	5.76E-06	mr1428_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
vg1200003632	NA	5.57E-15	mr1889_2	Ind_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
vg1200003632	NA	1.31E-09	mr1896_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
vg1200003632	NA	4.66E-14	mr1907_2	Ind_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
vg1200003632	NA	1.28E-12	mr1934_2	Ind_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