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Detailed information for vg0124756770:

Variant ID: vg0124756770 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24756770
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAATCCTTCCAAGGTCAGAAGTACAAGCACATGAAAATTGCACAGCAGCATAGGGTTTATTTCCTTTGCTTTTACAATCAGTGATCAGGTTTTGTTCC[A/T]
AAAATAAGTTTAGCTTTTATTGTGGATATTTGCAATCAAATGAACAGGAAACAACCTATACCTGTTTCAAATTAGAACTACTAGAGCGATGCATAGCCAT

Reverse complement sequence

ATGGCTATGCATCGCTCTAGTAGTTCTAATTTGAAACAGGTATAGGTTGTTTCCTGTTCATTTGATTGCAAATATCCACAATAAAAGCTAAACTTATTTT[T/A]
GGAACAAAACCTGATCACTGATTGTAAAAGCAAAGGAAATAAACCCTATGCTGCTGTGCAATTTTCATGTGCTTGTACTTCTGACCTTGGAAGGATTGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.90%	24.00%	0.06%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	31.00%	69.00%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	18.50%	81.40%	0.13%	0.00%	NA
Tropical Japonica	504	52.80%	47.20%	0.00%	0.00%	NA
Japonica Intermediate	241	24.90%	75.10%	0.00%	0.00%	NA
VI/Aromatic	96	37.50%	60.40%	2.08%	0.00%	NA
Intermediate	90	71.10%	28.90%	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
vg0124756770	A -> T	LOC_Os01g43320.1	intron_variant ; MODIFIER	silent_mutation	Average:66.255; most accessible tissue: Zhenshan97 root, score: 91.119	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)
vg0124756770	A	T	0.04	0.02	0.01	0.01	0.02	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124756770	NA	7.91E-11	mr1188	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
vg0124756770	3.34E-06	NA	mr1388	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
vg0124756770	3.14E-06	4.66E-08	mr1388	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
vg0124756770	NA	3.85E-06	mr1646	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
vg0124756770	NA	5.44E-28	mr1238_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
vg0124756770	NA	7.66E-25	mr1484_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
vg0124756770	NA	1.11E-06	mr1568_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
vg0124756770	NA	1.02E-19	mr1900_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
vg0124756770	NA	7.39E-20	mr1945_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