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Detailed information for vg0609100240:

Variant ID: vg0609100240 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9100240
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, T: 0.07, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

TTATGTAAGATGGTACCATTTTTCTCACGTTGGTTTAGACAGTGCACTTATTGTTGCGCATAGTGGGCTGGTGCTTACGTAAGATGAGACTTAGGTGGAG[G/T]
TTGGATAAGAGACTTAACTTTAGTCTCTGACACTAATTTAGAGTATTAAATATAGACTAATTACATAAATGAAAGCTAATTTGTGAGATAAATTTTTTAA

Reverse complement sequence

TTAAAAAATTTATCTCACAAATTAGCTTTCATTTATGTAATTAGTCTATATTTAATACTCTAAATTAGTGTCAGAGACTAAAGTTAAGTCTCTTATCCAA[C/A]
CTCCACCTAAGTCTCATCTTACGTAAGCACCAGCCCACTATGCGCAACAATAAGTGCACTGTCTAAACCAACGTGAGAAAAATGGTACCATCTTACATAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.80%	31.10%	0.13%	0.00%	NA
All Indica	2759	68.10%	31.70%	0.14%	0.00%	NA
All Japonica	1512	61.90%	38.00%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	58.50%	41.30%	0.17%	0.00%	NA
Indica II	465	94.00%	5.80%	0.22%	0.00%	NA
Indica III	913	55.10%	44.90%	0.00%	0.00%	NA
Indica Intermediate	786	75.30%	24.40%	0.25%	0.00%	NA
Temperate Japonica	767	28.60%	71.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	90.90%	8.70%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	17.80%	1.11%	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
vg0609100240	G -> T	LOC_Os06g15995.1	upstream_gene_variant ; 1686.0bp to feature; MODIFIER	silent_mutation	Average:78.708; most accessible tissue: Callus, score: 92.32	N	N	N	N
vg0609100240	G -> T	LOC_Os06g16000.1	upstream_gene_variant ; 503.0bp to feature; MODIFIER	silent_mutation	Average:78.708; most accessible tissue: Callus, score: 92.32	N	N	N	N
vg0609100240	G -> T	LOC_Os06g15990.1	downstream_gene_variant ; 3561.0bp to feature; MODIFIER	silent_mutation	Average:78.708; most accessible tissue: Callus, score: 92.32	N	N	N	N
vg0609100240	G -> T	LOC_Os06g15995-LOC_Os06g16000	intergenic_region ; MODIFIER	silent_mutation	Average:78.708; most accessible tissue: Callus, score: 92.32	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0609100240	G	T	-0.03	-0.04	-0.03	-0.01	-0.01	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609100240	NA	7.23E-14	Grain_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0609100240	NA	8.27E-06	mr1096	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
vg0609100240	7.89E-11	6.19E-20	mr1570	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
vg0609100240	8.20E-08	7.17E-12	mr1570	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
vg0609100240	NA	9.54E-09	mr1570	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
vg0609100240	1.71E-06	NA	mr1087_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
vg0609100240	NA	1.17E-13	mr1087_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
vg0609100240	NA	6.08E-06	mr1091_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
vg0609100240	NA	2.11E-07	mr1096_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
vg0609100240	NA	3.30E-10	mr1530_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
vg0609100240	1.60E-08	2.34E-12	mr1570_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
vg0609100240	1.15E-08	1.27E-16	mr1570_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