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Detailed information for vg1223000364:

Variant ID: vg1223000364 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23000364
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTGGAGCGGAGGCCGGCGGCGACGGCGATGGCGATGCAGTTGCTGGCGAGCTTGGCGAGCTCGGCGTCCTGCTTGGACATGAGCGGCGGGATGTCGCCG[T/C]
CGCGTTCCTCGAAGCCCTGGTCGCAGGTGTCGACGTCGGTGCGGGCCGTGTCGAGCATGGTGCCCGTCGTGTCCTTGTCGCCGGCGGCCATGGCCTTGTC

Reverse complement sequence

GACAAGGCCATGGCCGCCGGCGACAAGGACACGACGGGCACCATGCTCGACACGGCCCGCACCGACGTCGACACCTGCGACCAGGGCTTCGAGGAACGCG[A/G]
CGGCGACATCCCGCCGCTCATGTCCAAGCAGGACGCCGAGCTCGCCAAGCTCGCCAGCAACTGCATCGCCATCGCCGTCGCCGCCGGCCTCCGCTCCAGC

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	73.70%	0.10%	4.42%	21.71%	NA
All Indica	2759	86.40%	0.30%	3.52%	9.86%	NA
All Japonica	1512	50.20%	0.00%	6.28%	43.52%	NA
Aus	269	85.50%	0.00%	1.86%	12.64%	NA
Indica I	595	64.50%	0.00%	6.22%	29.24%	NA
Indica II	465	91.20%	0.00%	3.66%	5.16%	NA
Indica III	913	95.70%	0.80%	0.99%	2.52%	NA
Indica Intermediate	786	89.20%	0.00%	4.33%	6.49%	NA
Temperate Japonica	767	42.40%	0.00%	8.21%	49.41%	NA
Tropical Japonica	504	60.90%	0.00%	3.77%	35.32%	NA
Japonica Intermediate	241	52.70%	0.00%	5.39%	41.91%	NA
VI/Aromatic	96	51.00%	0.00%	8.33%	40.62%	NA
Intermediate	90	70.00%	0.00%	4.44%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223000364	T -> C	LOC_Os12g37480.1	missense_variant ; p.Asp197Gly; MODERATE	nonsynonymous_codon ; D197G	Average:80.161; most accessible tissue: Minghui63 panicle, score: 92.231	unknown	unknown	DELETERIOUS	0.02
vg1223000364	T -> DEL	LOC_Os12g37480.1	N	frameshift_variant	Average:80.161; most accessible tissue: Minghui63 panicle, score: 92.231	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)
vg1223000364	T	C	-0.04	-0.04	0.0	0.02	0.0	0.0