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Detailed information for vg1223130850:

Variant ID: vg1223130850 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 23130850
Reference Allele: CA	Alternative Allele: C,CAA,CAAAAA,CAAAA,CAAA,CAAAAAAAAA
Primary Allele: CA	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCACAAGACAGTCAGCATCCGCGACATAGGACGGCTCTGCGGCGTAGCGCCCTGGCGGCTGCCTCGACTCCCTTTGGCGTGCTCCGGTGAGGCAAAATGA[CA/C,CAA,CAAAAA,CAAAA,CAAA,CAAAAAAAAA]
AAAAAAACCTTCTCCGGCAAGCAGCGGATGATGGCGAGCATCGCTTGGCAGCGTTGCGTCGTCTACGGACTCAGGCGGCTCGACGACGTCCCCGACAACT

Reverse complement sequence

AGTTGTCGGGGACGTCGTCGAGCCGCCTGAGTCCGTAGACGACGCAACGCTGCCAAGCGATGCTCGCCATCATCCGCTGCTTGCCGGAGAAGGTTTTTTT[TG/G,TTG,TTTTTG,TTTTG,TTTG,TTTTTTTTTG]
TCATTTTGCCTCACCGGAGCACGCCAAAGGGAGTCGAGGCAGCCGCCAGGGCGCTACGCCGCAGAGCCGTCCTATGTCGCGGATGCTGACTGTCTTGTGC

Allele Frequencies:

Populations	Population Size	Frequency of CA(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.60%	2.40%	25.81%	27.55%	CAA: 0.51%; CAAAA: 0.06%; CAAAAAAAAA: 0.02%; CAAAAA: 0.02%
All Indica	2759	43.60%	0.80%	26.60%	28.60%	CAA: 0.43%
All Japonica	1512	50.90%	0.00%	21.56%	26.72%	CAA: 0.53%; CAAAA: 0.13%; CAAAAA: 0.07%; CAAAAAAAAA: 0.07%
Aus	269	17.10%	33.80%	30.48%	17.10%	CAA: 1.12%; CAAAA: 0.37%
Indica I	595	77.00%	0.20%	16.81%	6.05%	NA
Indica II	465	49.90%	0.60%	20.65%	28.82%	NA
Indica III	913	14.70%	0.70%	34.39%	49.29%	CAA: 0.99%
Indica Intermediate	786	48.20%	1.40%	28.50%	21.50%	CAA: 0.38%
Temperate Japonica	767	69.50%	0.00%	11.73%	17.47%	CAA: 0.78%; CAAAA: 0.26%; CAAAAAAAAA: 0.13%; CAAAAA: 0.13%
Tropical Japonica	504	31.50%	0.00%	32.34%	36.11%	NA
Japonica Intermediate	241	32.40%	0.00%	30.29%	36.51%	CAA: 0.83%
VI/Aromatic	96	7.30%	0.00%	44.79%	47.92%	NA
Intermediate	90	37.80%	3.30%	38.89%	18.89%	CAA: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223130850	CA -> C	LOC_Os12g37680.1	frameshift_variant ; p.Thr5fs; HIGH	frameshift_variant	Average:87.011; most accessible tissue: Minghui63 flag leaf, score: 99.571	N	N	N	N
vg1223130850	CA -> CAAAAA	LOC_Os12g37680.1	frameshift_variant ; p.Thr5fs; HIGH	frameshift_variant	Average:87.011; most accessible tissue: Minghui63 flag leaf, score: 99.571	N	N	N	N
vg1223130850	CA -> CAA	LOC_Os12g37680.1	frameshift_variant ; p.Thr5fs; HIGH	frameshift_variant	Average:87.011; most accessible tissue: Minghui63 flag leaf, score: 99.571	N	N	N	N
vg1223130850	CA -> CAAA	LOC_Os12g37680.1	frameshift_variant ; p.Thr5fs; HIGH	N	Average:87.011; most accessible tissue: Minghui63 flag leaf, score: 99.571	N	N	N	N
vg1223130850	CA -> CAAA	LOC_Os12g37690.1	downstream_gene_variant ; 4204.0bp to feature; MODIFIER	N	Average:87.011; most accessible tissue: Minghui63 flag leaf, score: 99.571	N	N	N	N
vg1223130850	CA -> CAAAA	LOC_Os12g37680.1	disruptive_inframe_insertion ; p.Lys4dup; MODERATE	inframe_variant	Average:87.011; most accessible tissue: Minghui63 flag leaf, score: 99.571	N	N	N	N
vg1223130850	CA -> CAAAAAAAAA	LOC_Os12g37680.1	frameshift_variant ; p.Thr5fs; HIGH	frameshift_variant	Average:87.011; most accessible tissue: Minghui63 flag leaf, score: 99.571	N	N	N	N
vg1223130850	CA -> DEL	LOC_Os12g37680.1	N	frameshift_variant	Average:87.011; most accessible tissue: Minghui63 flag leaf, score: 99.571	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)
vg1223130850	CA	C	-0.01	-0.04	-0.04	0.0	0.0	0.14
vg1223130850	CA	CAA	0.04	-0.01	-0.01	0.04	0.06	0.18
vg1223130850	CA	CAAA	0.19	0.08	0.09	0.08	0.15	0.2
vg1223130850	CA	CAAAA	0.2	0.11	0.13	0.1	0.19	0.12
vg1223130850	CA	CAAAA*	0.41	0.19	0.24	0.2	0.31	0.23