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Detailed information for vg0103847902:

Variant ID: vg0103847902 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3847902
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGGCCTCTGTCTGTTGCATTATCAATATAAGAGGTCAAATTAGTTTGTTTCTGGGGAATAATGTGTGAGCTCCACAGTACATCACTTTTTTGACAAAG[T/C]
TTTACATAGGAGATAAAGTTTTAGCTTTGATATCCCTGGTGGCTGGGTAGTTACTTAATTCTCTTGCATAGCTTCTTTCCATGTCATACGCCATATTCAC

Reverse complement sequence

GTGAATATGGCGTATGACATGGAAAGAAGCTATGCAAGAGAATTAAGTAACTACCCAGCCACCAGGGATATCAAAGCTAAAACTTTATCTCCTATGTAAA[A/G]
CTTTGTCAAAAAAGTGATGTACTGTGGAGCTCACACATTATTCCCCAGAAACAAACTAATTTGACCTCTTATATTGATAATGCAACAGACAGAGGCCCCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.10%	16.80%	0.02%	0.04%	NA
All Indica	2759	81.50%	18.40%	0.04%	0.07%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	7.40%	92.60%	0.00%	0.00%	NA
Indica I	595	52.30%	47.20%	0.17%	0.34%	NA
Indica II	465	93.80%	6.20%	0.00%	0.00%	NA
Indica III	913	92.40%	7.60%	0.00%	0.00%	NA
Indica Intermediate	786	83.70%	16.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0103847902	T -> DEL	N	N	silent_mutation	Average:55.311; most accessible tissue: Minghui63 flag leaf, score: 76.807	N	N	N	N
vg0103847902	T -> C	LOC_Os01g07950.1	downstream_gene_variant ; 2361.0bp to feature; MODIFIER	silent_mutation	Average:55.311; most accessible tissue: Minghui63 flag leaf, score: 76.807	N	N	N	N
vg0103847902	T -> C	LOC_Os01g07960.1	intron_variant ; MODIFIER	silent_mutation	Average:55.311; most accessible tissue: Minghui63 flag leaf, score: 76.807	N	N	N	N
vg0103847902	T -> C	LOC_Os01g07960.3	intron_variant ; MODIFIER	silent_mutation	Average:55.311; most accessible tissue: Minghui63 flag leaf, score: 76.807	N	N	N	N
vg0103847902	T -> C	LOC_Os01g07960.2	intron_variant ; MODIFIER	silent_mutation	Average:55.311; most accessible tissue: Minghui63 flag leaf, score: 76.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103847902	NA	6.19E-08	mr1038	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
vg0103847902	NA	1.29E-08	mr1389	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
vg0103847902	NA	4.41E-15	mr1874	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
vg0103847902	NA	2.19E-06	mr1038_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
vg0103847902	NA	2.88E-07	mr1389_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
vg0103847902	NA	3.07E-27	mr1874_2	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
vg0103847902	NA	1.14E-06	mr1874_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