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Detailed information for vg0100924740:

Variant ID: vg0100924740 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 924740
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TTATCATGTTCTGGACAGGACACCATCCTGTATCACCCAGTTCTAGGCTCCTGCAAGGTGACTGCAATATCTTACAAGCATGCTGCCATGTCCATCATCC[T/C]
GCTTGTAGATTCCACACCTCACTGCCCACTTCAGAAGCTCATCTCGACAAATTTATCAACTGATGTGTACAAACCTCAAAAATTGGAAGCTGCAAGCTTA

Reverse complement sequence

TAAGCTTGCAGCTTCCAATTTTTGAGGTTTGTACACATCAGTTGATAAATTTGTCGAGATGAGCTTCTGAAGTGGGCAGTGAGGTGTGGAATCTACAAGC[A/G]
GGATGATGGACATGGCAGCATGCTTGTAAGATATTGCAGTCACCTTGCAGGAGCCTAGAACTGGGTGATACAGGATGGTGTCCTGTCCAGAACATGATAA

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	62.00%	0.80%	2.64%	34.53%	NA
All Indica	2759	71.10%	0.60%	2.65%	25.59%	NA
All Japonica	1512	48.00%	1.10%	2.31%	48.54%	NA
Aus	269	55.80%	1.10%	4.83%	38.29%	NA
Indica I	595	44.00%	2.20%	8.40%	45.38%	NA
Indica II	465	94.40%	0.00%	0.00%	5.59%	NA
Indica III	913	72.50%	0.00%	0.11%	27.38%	NA
Indica Intermediate	786	76.30%	0.50%	2.80%	20.36%	NA
Temperate Japonica	767	71.30%	1.20%	1.96%	25.55%	NA
Tropical Japonica	504	10.90%	1.00%	3.57%	84.52%	NA
Japonica Intermediate	241	51.50%	1.20%	0.83%	46.47%	NA
VI/Aromatic	96	35.40%	0.00%	1.04%	63.54%	NA
Intermediate	90	64.40%	1.10%	3.33%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0100924740	T -> DEL	LOC_Os01g02710.1	N	frameshift_variant	Average:80.331; most accessible tissue: Zhenshan97 flag leaf, score: 95.842	N	N	N	N
vg0100924740	T -> C	LOC_Os01g02710.1	missense_variant ; p.Leu97Pro; MODERATE	nonsynonymous_codon ; L97P	Average:80.331; most accessible tissue: Zhenshan97 flag leaf, score: 95.842	unknown	unknown	TOLERATED	0.72

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)
vg0100924740	T	C	-0.01	0.0	0.0	-0.02	-0.02	-0.02