Upload 44 files (#2)

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Co-authored-by: Javier Mendoza Revilla <[email protected]>

.gitattributes

@@ -127,3 +127,6 @@ chromatin_access/sorghum_bicolor_test.fa filter=lfs diff=lfs merge=lfs -text
 pro_seq/m_esculenta_test.fa filter=lfs diff=lfs merge=lfs -text
 pro_seq/m_esculenta_train.fa filter=lfs diff=lfs merge=lfs -text
 pro_seq/m_esculenta_validation.fa filter=lfs diff=lfs merge=lfs -text
+Figures/Fig2_paneld1.txt filter=lfs diff=lfs merge=lfs -text
+Figures/Fig2_paneld2.txt filter=lfs diff=lfs merge=lfs -text
+Figures/Fig5_panela.txt filter=lfs diff=lfs merge=lfs -text

Figures/Fig2_panela.txt

@@ -0,0 +1,37 @@
+Species	Feature	Num
+A. thaliana	3'UTR	24315
+A. thaliana	5'UTR	3827
+A. thaliana	CDS	21226
+A. thaliana	exon	950
+A. thaliana	intron	9144
+A. thaliana	3'UTRext	7613
+C. reinhardtii	3'UTR	21535
+C. reinhardtii	5'UTR	816
+C. reinhardtii	CDS	1112
+C. reinhardtii	exon	0
+C. reinhardtii	intron	883
+C. reinhardtii	3'UTRext	9294
+M. truncatula	3'UTR	8734
+M. truncatula	5'UTR	470
+M. truncatula	CDS	3278
+M. truncatula	exon	0
+M. truncatula	intron	1871
+M. truncatula	3'UTRext	4356
+O. sativa (Ind)	3'UTR	0
+O. sativa (Ind)	5'UTR	0
+O. sativa (Ind)	CDS	1057
+O. sativa (Ind)	exon	0
+O. sativa (Ind)	intron	5556
+O. sativa (Ind)	3'UTRext	31693
+O. sativa (Jap)	3'UTR	17888
+O. sativa (Jap)	5'UTR	744
+O. sativa (Jap)	CDS	1443
+O. sativa (Jap)	exon	0
+O. sativa (Jap)	intron	4927
+O. sativa (Jap)	3'UTRext	21949
+T. pratense	3'UTR	15411
+T. pratense	5'UTR	800
+T. pratense	CDS	9726
+T. pratense	exon	170
+T. pratense	intron	5291
+T. pratense	3'UTRext	10301

Figures/Fig2_panelbc.txt

@@ -0,0 +1,21 @@
+Chrom	Label	Count
+chr1	non-acceptor	563764
+chr1	acceptor	20011
+chr2	non-acceptor	333524
+chr2	acceptor	11764
+chr3	non-acceptor	426301
+chr3	acceptor	15063
+chr4	non-acceptor	322825
+chr4	acceptor	11592
+chr5	non-acceptor	511484
+chr5	acceptor	18441
+chr1	non-donor	866124
+chr1	donor	19970
+chr2	non-donor	513532
+chr2	donor	11725
+chr3	non-donor	655110
+chr3	donor	15017
+chr4	non-donor	494988
+chr4	donor	11568
+chr5	non-donor	782180
+chr5	donor	18379

Figures/Fig2_paneld1.txt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:79649a4ddc6fa09ee7e1ade9383c629c8264f00ccfe8597470b734896556e0bf
+size 42089628

Figures/Fig2_paneld2.txt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9009561c0c756edc850236a38e1d1b7fe431d87b6c7ab675b18b4024ec4a9183
+size 42609765

Figures/Fig3_panele.txt

@@ -0,0 +1,13 @@
+Species	Model	Type	R2
+A. thaliana	Maize model	AgroNT	0.62
+S. bicolor	Maize model	AgroNT	0.68
+Z. mays	Maize model	AgroNT	0.71
+A. thaliana	Tobacco model	AgroNT	0.62
+S. bicolor	Tobacco model	AgroNT	0.74
+Z. mays	Tobacco model	AgroNT	0.75
+A. thaliana	Maize model	CNN (Jores et al.)	0.58
+S. bicolor	Maize model	CNN (Jores et al.)	0.65
+Z. mays	Maize model	CNN (Jores et al.)	0.69
+A. thaliana	Tobacco model	CNN (Jores et al.)	0.57
+S. bicolor	Tobacco model	CNN (Jores et al.)	0.71
+Z. mays	Tobacco model	CNN (Jores et al.)	0.73

Figures/Fig3_panelf.txt

@@ -0,0 +1,13 @@
+Species	Model	Type	R2
+A. thaliana	Maize model	AgroNT	0.69
+GC	Maize model	AgroNT	0.68
+Z. mays	Maize model	AgroNT	0.65
+A. thaliana	Tobacco model	AgroNT	0.77
+GC	Tobacco model	AgroNT	0.67
+Z. mays	Tobacco model	AgroNT	0.76
+A. thaliana	Maize model	CNN (Gorjifard et al.)	0.68
+GC	Maize model	CNN (Gorjifard et al.)	0.64
+Z. mays	Maize model	CNN (Gorjifard et al.)	0.67
+A. thaliana	Tobacco model	CNN (Gorjifard et al.)	0.77
+GC	Tobacco model	CNN (Gorjifard et al.)	0.65
+Z. mays	Tobacco model	CNN (Gorjifard et al.)	0.76

Figures/Fig4_panelb.txt

@@ -0,0 +1,191 @@
+Species	Tissue	Method	AUC
+Z. mays	Zmays_ear_big_bottom_1	AgroNT	0.981893775458721
+Z. mays	Zmays_ear_big_bottom_1	DeepSEA	0.9807
+Z. mays	Zmays_ear_big_bottom_2	AgroNT	0.983912174594928
+Z. mays	Zmays_ear_big_bottom_2	DeepSEA	0.9828
+Z. mays	Zmays_ear_big_top_1	AgroNT	0.980965753226404
+Z. mays	Zmays_ear_big_top_1	DeepSEA	0.9802
+Z. mays	Zmays_ear_big_top_2	AgroNT	0.983192363826982
+Z. mays	Zmays_ear_big_top_2	DeepSEA	0.9826
+Z. mays	Zmays_ear_small_1	AgroNT	0.981633119983466
+Z. mays	Zmays_ear_small_1	DeepSEA	0.98
+Z. mays	Zmays_ear_small_2	AgroNT	0.981918011278322
+Z. mays	Zmays_ear_small_2	DeepSEA	0.9815
+Z. mays	Zmays_flag_leaf_1	AgroNT	0.979817688893831
+Z. mays	Zmays_flag_leaf_1	DeepSEA	0.9823
+Z. mays	Zmays_flag_leaf_2	AgroNT	0.979793357683983
+Z. mays	Zmays_flag_leaf_2	DeepSEA	0.9823
+Z. mays	Zmays_flower_1	AgroNT	0.986516769179244
+Z. mays	Zmays_flower_1	DeepSEA	0.9827
+Z. mays	Zmays_flower_2	AgroNT	0.986648079267573
+Z. mays	Zmays_flower_2	DeepSEA	0.9888
+Z. mays	Zmays_root_1	AgroNT	0.98366877408458
+Z. mays	Zmays_root_1	DeepSEA	0.9847
+Z. mays	Zmays_root_2	AgroNT	0.983761544892374
+Z. mays	Zmays_root_2	DeepSEA	0.9862
+Z. mays	Zmays_root_3	AgroNT	0.978893882607849
+Z. mays	Zmays_root_3	DeepSEA	0.9813
+Z. mays	Zmays_tassel_bottom_1	AgroNT	0.984366920979795
+Z. mays	Zmays_tassel_bottom_1	DeepSEA	0.9835
+Z. mays	Zmays_tassel_bottom_2	AgroNT	0.983714655209693
+Z. mays	Zmays_tassel_bottom_2	DeepSEA	0.9826
+Z. mays	Zmays_tassel_top_1	AgroNT	0.981452565673348
+Z. mays	Zmays_tassel_top_1	DeepSEA	0.9823
+Z. mays	Zmays_young_leaf_1	AgroNT	0.984966182571289
+Z. mays	Zmays_young_leaf_1	DeepSEA	0.9866
+Z. mays	Zmays_young_leaf_2	AgroNT	0.986670289174259
+Z. mays	Zmays_young_leaf_2	DeepSEA	0.988
+Z. mays	Zmays_young_leaf_3	AgroNT	0.978924277113606
+Z. mays	Zmays_young_leaf_3	DeepSEA	0.9814
+S. italica	Sitalica_flag_leaf_1	AgroNT	0.944024138159233
+S. italica	Sitalica_flag_leaf_1	DeepSEA	0.9475
+S. italica	Sitalica_flag_leaf_2	AgroNT	0.944368499972782
+S. italica	Sitalica_flag_leaf_2	DeepSEA	0.9491
+S. italica	Sitalica_flower_1	AgroNT	0.95310049075726
+S. italica	Sitalica_flower_1	DeepSEA	0.9497
+S. italica	Sitalica_flower_2	AgroNT	0.953664147176581
+S. italica	Sitalica_flower_2	DeepSEA	0.9492
+S. italica	Sitalica_panicle_1	AgroNT	0.953544404251039
+S. italica	Sitalica_panicle_1	DeepSEA	0.9489
+S. italica	Sitalica_panicle_2	AgroNT	0.956185429551665
+S. italica	Sitalica_panicle_2	DeepSEA	0.9515
+S. italica	Sitalica_root_1	AgroNT	0.982534830071808
+S. italica	Sitalica_root_1	DeepSEA	0.9806
+S. italica	Sitalica_young_leaf_1	AgroNT	0.970654176829444
+S. italica	Sitalica_young_leaf_1	DeepSEA	0.9734
+S. italica	Sitalica_young_leaf_2	AgroNT	0.960840181820109
+S. italica	Sitalica_young_leaf_2	DeepSEA	0.9611
+S. bicolor	Sorghum_flag_leaf_1	AgroNT	0.974832701363744
+S. bicolor	Sorghum_flag_leaf_1	DeepSEA	0.977
+S. bicolor	Sorghum_flag_leaf_2	AgroNT	0.97042614544364
+S. bicolor	Sorghum_flag_leaf_2	DeepSEA	0.9753
+S. bicolor	Sorghum_flower_1	AgroNT	0.968993168619242
+S. bicolor	Sorghum_flower_1	DeepSEA	0.9721
+S. bicolor	Sorghum_flower_2	AgroNT	0.969920665370966
+S. bicolor	Sorghum_flower_2	DeepSEA	0.9714
+S. bicolor	Sorghum_lemma_1	AgroNT	0.973795562902938
+S. bicolor	Sorghum_lemma_1	DeepSEA	0.9745
+S. bicolor	Sorghum_lemma_2	AgroNT	0.966884736086807
+S. bicolor	Sorghum_lemma_2	DeepSEA	0.972
+S. bicolor	Sorghum_panicle_bottom_1	AgroNT	0.969094439691713
+S. bicolor	Sorghum_panicle_bottom_1	DeepSEA	0.9691
+S. bicolor	Sorghum_panicle_bottom_2	AgroNT	0.963600554336402
+S. bicolor	Sorghum_panicle_bottom_2	DeepSEA	0.966
+S. bicolor	Sorghum_panicle_top_1	AgroNT	0.979871200130056
+S. bicolor	Sorghum_panicle_top_1	DeepSEA	0.9778
+S. bicolor	Sorghum_panicle_top_2	AgroNT	0.978069551723402
+S. bicolor	Sorghum_panicle_top_2	DeepSEA	0.9776
+S. bicolor	Sorghum_root_1	AgroNT	0.990285421719328
+S. bicolor	Sorghum_root_1	DeepSEA	0.9907
+S. bicolor	Sorghum_root_2	AgroNT	0.967368650288689
+S. bicolor	Sorghum_root_2	DeepSEA	0.9671
+S. bicolor	Sorghum_young_leaf_1	AgroNT	0.983546550899923
+S. bicolor	Sorghum_young_leaf_1	DeepSEA	0.9841
+S. bicolor	Sorghum_young_leaf_2	AgroNT	0.985633959206328
+S. bicolor	Sorghum_young_leaf_2	DeepSEA	0.9856
+O. sativa	MH63_flag_leaf_1	AgroNT	0.953557915779257
+O. sativa	MH63_flag_leaf_1	DeepSEA	0.9345
+O. sativa	MH63_flag_leaf_2	AgroNT	0.949630325952582
+O. sativa	MH63_flag_leaf_2	DeepSEA	0.9508
+O. sativa	MH63_flower_1	AgroNT	0.941272640332567
+O. sativa	MH63_flower_1	DeepSEA	0.9746
+O. sativa	MH63_flower_2	AgroNT	0.940889495879432
+O. sativa	MH63_flower_2	DeepSEA	0.981
+O. sativa	MH63_lemma_1	AgroNT	0.960587051768769
+O. sativa	MH63_lemma_1	DeepSEA	0.9458
+O. sativa	MH63_lemma_2	AgroNT	0.955992283046744
+O. sativa	MH63_lemma_2	DeepSEA	0.9478
+O. sativa	MH63_panicle_1	AgroNT	0.96694647990786
+O. sativa	MH63_panicle_1	DeepSEA	0.9636
+O. sativa	MH63_panicle_2	AgroNT	0.976575958888608
+O. sativa	MH63_panicle_2	DeepSEA	0.9686
+O. sativa	MH63_panicle_3	AgroNT	0.967295262054253
+O. sativa	MH63_panicle_3	DeepSEA	0.9708
+O. sativa	MH63_panicle_4	AgroNT	0.962823534116396
+O. sativa	MH63_panicle_4	DeepSEA	0.9573
+O. sativa	MH63_panicle_5	AgroNT	0.961028854238987
+O. sativa	MH63_panicle_5	DeepSEA	0.9588
+O. sativa	MH63_root_1	AgroNT	0.95042864895822
+O. sativa	MH63_root_1	DeepSEA	0.9535
+O. sativa	MH63_root_2	AgroNT	0.9524977551959
+O. sativa	MH63_root_2	DeepSEA	0.9563
+O. sativa	MH63_young_leaf_1	AgroNT	0.942603068013723
+O. sativa	MH63_young_leaf_1	DeepSEA	0.9457
+O. sativa	MH63_young_leaf_2	AgroNT	0.963966771336426
+O. sativa	MH63_young_leaf_2	DeepSEA	0.952
+O. sativa	ZS97_flag_leaf_1	AgroNT	0.953557915779257
+O. sativa	ZS97_flag_leaf_1	DeepSEA	0.95
+O. sativa	ZS97_flag_leaf_2	AgroNT	0.949630325952582
+O. sativa	ZS97_flag_leaf_2	DeepSEA	0.9468
+O. sativa	ZS97_flower_1	AgroNT	0.941272640332567
+O. sativa	ZS97_flower_1	DeepSEA	0.9383
+O. sativa	ZS97_flower_2	AgroNT	0.940889495879432
+O. sativa	ZS97_flower_2	DeepSEA	0.9382
+O. sativa	ZS97_lemma_1	AgroNT	0.960587051768769
+O. sativa	ZS97_lemma_1	DeepSEA	0.9599
+O. sativa	ZS97_lemma_2	AgroNT	0.955992283046744
+O. sativa	ZS97_lemma_2	DeepSEA	0.9563
+O. sativa	ZS97_panicle_1	AgroNT	0.96694647990786
+O. sativa	ZS97_panicle_1	DeepSEA	0.9616
+O. sativa	ZS97_panicle_2	AgroNT	0.976575958888608
+O. sativa	ZS97_panicle_2	DeepSEA	0.9738
+O. sativa	ZS97_panicle_3	AgroNT	0.967295262054253
+O. sativa	ZS97_panicle_3	DeepSEA	0.9646
+O. sativa	ZS97_panicle_4	AgroNT	0.962823534116396
+O. sativa	ZS97_panicle_4	DeepSEA	0.959
+O. sativa	ZS97_panicle_5	AgroNT	0.961028854238987
+O. sativa	ZS97_panicle_5	DeepSEA	0.955
+O. sativa	ZS97_root_1	AgroNT	0.95042864895822
+O. sativa	ZS97_root_1	DeepSEA	0.9495
+O. sativa	ZS97_root_2	AgroNT	0.9524977551959
+O. sativa	ZS97_root_2	DeepSEA	0.9504
+O. sativa	ZS97_young_leaf_1	AgroNT	0.942603068013723
+O. sativa	ZS97_young_leaf_1	DeepSEA	0.9465
+O. sativa	ZS97_young_leaf_2	AgroNT	0.963966771336426
+O. sativa	ZS97_young_leaf_2	DeepSEA	0.9603
+B. distachyon	flag_leaf_1	AgroNT	0.943395959465956
+B. distachyon	flag_leaf_1	DeepSEA	0.9386
+B. distachyon	flag_leaf_2	AgroNT	0.944775955433103
+B. distachyon	flag_leaf_2	DeepSEA	0.9384
+B. distachyon	flower_1	AgroNT	0.957222682628638
+B. distachyon	flower_1	DeepSEA	0.9522
+B. distachyon	flower_2	AgroNT	0.962451565529302
+B. distachyon	flower_2	DeepSEA	0.9598
+B. distachyon	panicle_1	AgroNT	0.959575443197348
+B. distachyon	panicle_1	DeepSEA	0.9529
+B. distachyon	root_1	AgroNT	0.966645451400899
+B. distachyon	root_1	DeepSEA	0.9571
+B. distachyon	root_2	AgroNT	0.957868390949404
+B. distachyon	root_2	DeepSEA	0.9551
+B. distachyon	young_leaf_1	AgroNT	0.949881344630109
+B. distachyon	young_leaf_1	DeepSEA	0.9474
+B. distachyon	young_leaf_2	AgroNT	0.963195725341801
+B. distachyon	young_leaf_2	DeepSEA	0.9524
+A. thaliana	7days_leaf_rep1	AgroNT	0.924384292823498
+A. thaliana	7days_leaf_rep1	DeepSEA	0.9214
+A. thaliana	7days_leaf_rep2	AgroNT	0.940838807358043
+A. thaliana	7days_leaf_rep2	DeepSEA	0.9397
+A. thaliana	mesophyll_rep1	AgroNT	0.953978841461623
+A. thaliana	mesophyll_rep1	DeepSEA	0.9499
+A. thaliana	mesophyll_rep2	AgroNT	0.952322992209123
+A. thaliana	mesophyll_rep2	DeepSEA	0.9456
+A. thaliana	mesophyll_rep3	AgroNT	0.951822940113686
+A. thaliana	mesophyll_rep3	DeepSEA	0.9493
+A. thaliana	root_hair_rep1	AgroNT	0.935826444576565
+A. thaliana	root_hair_rep1	DeepSEA	0.9341
+A. thaliana	root_hair_rep2	AgroNT	0.948641786084109
+A. thaliana	root_hair_rep2	DeepSEA	0.9482
+A. thaliana	root_non_hair_rep1	AgroNT	0.942184075232078
+A. thaliana	root_non_hair_rep1	DeepSEA	0.9378
+A. thaliana	root_non_hair_rep2	AgroNT	0.9455757148958
+A. thaliana	root_non_hair_rep2	DeepSEA	0.9438
+A. thaliana	root_tip_rep1	AgroNT	0.942864493452685
+A. thaliana	root_tip_rep1	DeepSEA	0.9515
+A. thaliana	root_tip_rep2	AgroNT	0.914008370410249
+A. thaliana	root_tip_rep2	DeepSEA	0.9163
+A. thaliana	stem_rep1	AgroNT	0.955013217684825
+A. thaliana	stem_rep1	DeepSEA	0.9502
+A. thaliana	stem_rep2	AgroNT	0.952474858182249
+A. thaliana	stem_rep2	DeepSEA	0.949
+A. thaliana	stem_rep3	AgroNT	0.951076943957884
+A. thaliana	stem_rep3	DeepSEA	0.9451

Figures/Fig5_panela.txt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:461c9e9430d20b6cd7f0cdb3b05ad264d58e1b69a15bda237dcd3ef008c0fe73
+size 13864400

Figures/Fig6_panelb.txt

@@ -0,0 +1,6 @@
+Variation	R2
+5kb US - 1kb DS	0.621
+4kb US - 2kb DS	0.645809
+3kb US - 3kb DS	0.659964
+2kb US - 4kb DS	0.657784
+1kb US - 5kb DS	0.661819

Figures/Fig6_panelc.txt

@@ -0,0 +1,47 @@
+Tissue	Variation	R2
+Root maturation zone	5kb US - 1kb DS	0.646219067243882
+Root elongation zone	5kb US - 1kb DS	0.613524896464522
+Root cortex	5kb US - 1kb DS	0.578358455733256
+Vegetative meristem	5kb US - 1kb DS	0.669993503216862
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+Endosperm crown	5kb US - 1kb DS	0.592805880599955
+Symmetrical division	5kb US - 1kb DS	0.658537665778199
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+Growth zone	5kb US - 1kb DS	0.639230824745207
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+Embryos	5kb US - 1kb DS	0.624652469376995
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+6.8 mm from ear tip	5kb US - 1kb DS	0.664358479872003
+2.4 mm from ear tip	5kb US - 1kb DS	0.668339614777341
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+Silks	5kb US - 1kb DS	0.610204476616703
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+Internode (7.8)	5kb US - 1kb DS	0.677069027420533
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+Root elongation zone	1kb US - 5kb DS	0.660089334320339
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+Vegetative meristem	1kb US - 5kb DS	0.701258766875842
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+Pericarp and aleurone	1kb US - 5kb DS	0.626868906344587
+Endosperm crown	1kb US - 5kb DS	0.631253455951277
+Symmetrical division	1kb US - 5kb DS	0.704309725260427
+Stomatal division	1kb US - 5kb DS	0.689357925511412
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+Embryos (20 Days)	1kb US - 5kb DS	0.686186907523153
+Embryos	1kb US - 5kb DS	0.665973906993976
+Germinating kernels	1kb US - 5kb DS	0.666933631719764
+Mature leaf tissue	1kb US - 5kb DS	0.604542688821447
+6.8 mm from ear tip	1kb US - 5kb DS	0.703620463545164
+2.4 mm from ear tip	1kb US - 5kb DS	0.707748064905367
+Primary root	1kb US - 5kb DS	0.668010231450032
+Secondary root	1kb US - 5kb DS	0.67491028488731
+Mature pollen	1kb US - 5kb DS	0.420681345188956
+Silks	1kb US - 5kb DS	0.641837225832962
+Mature female spikelets	1kb US - 5kb DS	0.688546636445079
+Internode (6.7)	1kb US - 5kb DS	0.708113345897187
+Internode (7.8)	1kb US - 5kb DS	0.708893025344515

Figures/Fig7_panela.txt

@@ -0,0 +1,13 @@
+Species	BinLabel	Ratio	RatioLCI	RatioUCI
+A. thaliana	<0.001	1.80417031573512	1.79421122117692	1.81321931733638
+A. thaliana	0.001-
+0.01	1.4763317224907	1.46760341533666	1.48427906135701
+A. thaliana	0.01-
+0.05	1.09434766849321	1.08411450726465	1.10372451878627
+A. thaliana	>0.05	0.74763122711155	0.741111647431835	0.753363306896884
+O. sativa	0.001-
+0.01	1.46922601186522	1.45328782528876	1.48447763257969
+O. sativa	<0.001	1.60192007144452	1.55255380932752	1.67003041483845
+O. sativa	0.01-
+0.05	1.32297667390688	1.30549882835489	1.34443622916762
+O. sativa	>0.05	1.22248373586318	1.21174568636103	1.23179399122349

Figures/Fig7_panelb.txt

@@ -0,0 +1,161 @@
+Species	BinLabel	Score	Cutoff	OR	ORLCI	ORUCI
+A. thaliana	0.001-0.01	GPN	0.01	2.79589374972583	2.65402406918302	2.94648832053553
+A. thaliana	<0.001	GPN	0.01	3.92476063722532	3.73003020997533	4.13140987300125
+O. sativa	0.001-0.01	GPN	0.01	1.78372157580633	1.73685975872899	1.8318793763113
+O. sativa	<0.001	GPN	0.01	3.11171004981781	2.94106822844044	3.29048630724921
+A. thaliana	0.001-0.01	LLR	0.01	2.02398349853504	1.9377917334414	2.11453215792092
+A. thaliana	<0.001	LLR	0.01	2.18601166256716	2.09456678363459	2.28230181199414
+O. sativa	0.001-0.01	LLR	0.01	2.16548807032713	2.1071480585774	2.22542085682122
+O. sativa	<0.001	LLR	0.01	8.2639173295073	7.91167022064462	8.62825790565756
+A. thaliana	0.001-0.01	dot product (layer 11)	0.01	2.39245013686122	2.28765733266279	2.5025932512594
+A. thaliana	<0.001	dot product (layer 11)	0.01	2.05662206960722	1.96701339971264	2.15123790981399
+O. sativa	0.001-0.01	dot product (layer 11)	0.01	1.80929616301833	1.76134591740048	1.85888615688131
+O. sativa	<0.001	dot product (layer 11)	0.01	10.9123215496555	10.4841389325897	11.3590983782801
+A. thaliana	0.001-0.01	dot product (layer 21)	0.01	1.9866399760306	1.9051245842422	2.07208934992022
+A. thaliana	<0.001	dot product (layer 21)	0.01	1.71927938362758	1.64902467710638	1.79317196177141
+O. sativa	0.001-0.01	dot product (layer 21)	0.01	3.33270424232566	3.237244254904	3.43129580579134
+O. sativa	<0.001	dot product (layer 21)	0.01	26.8675350565658	25.8449300106299	27.8827570590091
+A. thaliana	0.001-0.01	dot product (layer 31)	0.01	2.25854597369053	2.16205087820968	2.35991705032605
+A. thaliana	<0.001	dot product (layer 31)	0.01	1.89739397050903	1.81649190389093	1.98262249946846
+O. sativa	0.001-0.01	dot product (layer 31)	0.01	2.33684164561244	2.27318229095661	2.40231430379639
+O. sativa	<0.001	dot product (layer 31)	0.01	17.0698149322323	16.4267094445558	17.7307911102106
+A. thaliana	0.001-0.01	dot product (layer 40)	0.01	1.80494686959544	1.73285787239587	1.88029800499497
+A. thaliana	<0.001	dot product (layer 40)	0.01	1.61202761589844	1.54809671871742	1.67922745193526
+O. sativa	0.001-0.01	dot product (layer 40)	0.01	1.68633615196124	1.64110291876775	1.73301730246615
+O. sativa	<0.001	dot product (layer 40)	0.01	10.444299089724	10.0400574142299	10.8630741595171
+A. thaliana	0.001-0.01	phyloP	0.01	2.20207202102618	2.10380149721509	2.30567529695017
+A. thaliana	<0.001	phyloP	0.01	2.88798892256567	2.76196939195001	3.02075853654835
+O. sativa	0.001-0.01	phyloP	0.01	1.72702832638307	1.68231599074119	1.77303290817394
+O. sativa	<0.001	phyloP	0.01	0.840498307365427	0.761705530415916	0.925423940661311
+A. thaliana	0.001-0.01	phastCons	0.01	1.89308656025406	1.81158220362467	1.97866756734878
+A. thaliana	<0.001	phastCons	0.01	2.43942621345622	2.33720482809442	2.5468632305519
+O. sativa	0.001-0.01	phastCons	0.01	1.48288209164138	1.44488227970568	1.52198135857454
+O. sativa	<0.001	phastCons	0.01	0.468813407427246	0.413601445256946	0.52941794983114
+A. thaliana	0.001-0.01	GPN	0.02	2.48596852803267	2.40170202953465	2.57412793675262
+A. thaliana	<0.001	GPN	0.02	3.2627913321495	3.15439890855922	3.37589682928079
+O. sativa	0.001-0.01	GPN	0.02	1.5875395767333	1.5580151386903	1.61766713719248
+O. sativa	<0.001	GPN	0.02	2.46374425190682	2.36023095271571	2.57097841315927
+A. thaliana	0.001-0.01	LLR	0.02	1.83214271189839	1.77836491386574	1.88764535979103
+A. thaliana	<0.001	LLR	0.02	1.98228633427978	1.92525662120697	2.04144490458804
+O. sativa	0.001-0.01	LLR	0.02	2.05677217734568	2.01745843115565	2.0967133344759
+O. sativa	<0.001	LLR	0.02	6.93089846489104	6.70792989353286	7.15815844515565
+A. thaliana	0.001-0.01	dot product (layer 11)	0.02	2.06029218905194	1.99970136839312	2.12288798120994
+A. thaliana	<0.001	dot product (layer 11)	0.02	1.74799221790295	1.69674592834804	1.80115171926689
+O. sativa	0.001-0.01	dot product (layer 11)	0.02	1.75650404635071	1.72332235417785	1.79040921062824
+O. sativa	<0.001	dot product (layer 11)	0.02	9.95567894761612	9.66630634957815	10.2566647523147
+A. thaliana	0.001-0.01	dot product (layer 21)	0.02	1.66772753801108	1.62198729895713	1.71479149522291
+A. thaliana	<0.001	dot product (layer 21)	0.02	1.43132137560334	1.39225805390371	1.47171556185624
+O. sativa	0.001-0.01	dot product (layer 21)	0.02	2.58194466923083	2.53115419626317	2.63400826315577
+O. sativa	<0.001	dot product (layer 21)	0.02	20.3372291805836	19.7786950774532	20.9161269585403
+A. thaliana	0.001-0.01	dot product (layer 31)	0.02	2.02067748152562	1.96156677930071	2.08177474910558
+A. thaliana	<0.001	dot product (layer 31)	0.02	1.69058921674105	1.64120874248772	1.7417567494896
+O. sativa	0.001-0.01	dot product (layer 31)	0.02	2.2170527771336	2.17410007756911	2.26076038420915
+O. sativa	<0.001	dot product (layer 31)	0.02	15.9136510962947	15.4680775345836	16.3752779601244
+A. thaliana	0.001-0.01	dot product (layer 40)	0.02	1.58208848846697	1.53936244041925	1.62627450497646
+A. thaliana	<0.001	dot product (layer 40)	0.02	1.40478831954751	1.36708630413452	1.44377781150719
+O. sativa	0.001-0.01	dot product (layer 40)	0.02	1.64561226400604	1.61439113913757	1.6775716636048
+O. sativa	<0.001	dot product (layer 40)	0.02	9.26411600110014	8.99649325149299	9.53681409731375
+A. thaliana	0.001-0.01	phyloP	0.02	2.28451626067308	2.21121292738807	2.36065164852852
+A. thaliana	<0.001	phyloP	0.02	2.99526221515086	2.90145006548384	3.09253188797344
+O. sativa	0.001-0.01	phyloP	0.02	1.6668345334367	1.63994611966399	1.69438994520926
+O. sativa	<0.001	phyloP	0.02	0.836108399355207	0.787260247035125	0.887289328198364
+A. thaliana	0.001-0.01	phastCons	0.02	1.66240335236207	1.61383923016009	1.71275373343627
+A. thaliana	<0.001	phastCons	0.02	2.11713636728554	2.05701236857512	2.17952271285749
+O. sativa	0.001-0.01	phastCons	0.02	1.29302099700534	1.2693435437887	1.31723383291322
+O. sativa	<0.001	phastCons	0.02	0.439110007793609	0.402186299016245	0.478569803627006
+A. thaliana	0.001-0.01	GPN	0.03	2.33434121175978	2.27134685221323	2.39920588272483
+A. thaliana	<0.001	GPN	0.03	2.91670361477971	2.83965420882223	2.99605687495373
+O. sativa	0.001-0.01	GPN	0.03	1.4774203538699	1.45489745107115	1.50044433885433
+O. sativa	<0.001	GPN	0.03	2.11743742897935	2.04048688120762	2.19657676743216
+A. thaliana	0.001-0.01	LLR	0.03	1.71519899482058	1.6748686273663	1.75650026365398
+A. thaliana	<0.001	LLR	0.03	1.83440438137437	1.79222909917478	1.8780615482461
+O. sativa	0.001-0.01	LLR	0.03	1.97262905812463	1.94183051941307	2.00382938251295
+O. sativa	<0.001	LLR	0.03	6.16476994532928	5.99513927792258	6.33963184971565
+A. thaliana	0.001-0.01	dot product (layer 11)	0.03	1.84074777960111	1.79797061736989	1.88456560511542
+A. thaliana	<0.001	dot product (layer 11)	0.03	1.56614264033364	1.52988699327701	1.60350318325963
+O. sativa	0.001-0.01	dot product (layer 11)	0.03	1.71702344636813	1.69041914839738	1.74417696021837
+O. sativa	<0.001	dot product (layer 11)	0.03	9.65532740890558	9.4172637147712	9.89980237092704
+A. thaliana	0.001-0.01	dot product (layer 21)	0.03	1.51350093486639	1.48058513001606	1.54738759896126
+A. thaliana	<0.001	dot product (layer 21)	0.03	1.31337085913953	1.28487387272825	1.34261309872009
+O. sativa	0.001-0.01	dot product (layer 21)	0.03	2.32303980284168	2.2860555265821	2.36081094368585
+O. sativa	<0.001	dot product (layer 21)	0.03	17.7632678195676	17.3414325255972	18.1801760109056
+A. thaliana	0.001-0.01	dot product (layer 31)	0.03	1.85124326373307	1.80816934593179	1.89549127441719
+A. thaliana	<0.001	dot product (layer 31)	0.03	1.55040981663768	1.51447529879647	1.5874187718904
+O. sativa	0.001-0.01	dot product (layer 31)	0.03	2.12739104377944	2.09363895856261	2.161608259201
+O. sativa	<0.001	dot product (layer 31)	0.03	15.1689295147715	14.8163197162614	15.5432745511529
+A. thaliana	0.001-0.01	dot product (layer 40)	0.03	1.47376172667361	1.44184029224461	1.50662582440822
+A. thaliana	<0.001	dot product (layer 40)	0.03	1.322352464244	1.29391030299951	1.35157332722699
+O. sativa	0.001-0.01	dot product (layer 40)	0.03	1.58698174002996	1.56234493435694	1.61216997817258
+O. sativa	<0.001	dot product (layer 40)	0.03	8.35030732066262	8.14197798549785	8.56289797378876
+A. thaliana	0.001-0.01	phyloP	0.03	2.18407422566129	2.1266486273253	2.24332957314268
+A. thaliana	<0.001	phyloP	0.03	2.83435717922493	2.76123046757969	2.90934799380533
+O. sativa	0.001-0.01	phyloP	0.03	1.64183476756535	1.61692077037694	1.66732074370854
+O. sativa	<0.001	phyloP	0.03	0.807959936278909	0.763109529728135	0.854848844010782
+A. thaliana	0.001-0.01	phastCons	0.03	1.58260988659647	1.54547666514553	1.62097987213968
+A. thaliana	<0.001	phastCons	0.03	1.98508645816788	1.93985441957779	2.03180247683594
+O. sativa	0.001-0.01	phastCons	0.03	1.21750733649667	1.19908862125606	1.23623365064688
+O. sativa	<0.001	phastCons	0.03	0.448838802334234	0.418569113109332	0.480740067321972
+A. thaliana	0.001-0.01	GPN	0.04	2.19130490941388	2.14160395923093	2.24242742790748
+A. thaliana	<0.001	GPN	0.04	2.65346582461006	2.59419959003218	2.71397940681267
+O. sativa	0.001-0.01	GPN	0.04	1.40078499416436	1.38216238525556	1.4196225203297
+O. sativa	<0.001	GPN	0.04	1.89595067691544	1.83373011605294	1.95993711731558
+A. thaliana	0.001-0.01	LLR	0.04	1.62348319757259	1.59095452955447	1.65667715044617
+A. thaliana	<0.001	LLR	0.04	1.72472348751822	1.69096273390546	1.75959295927223
+O. sativa	0.001-0.01	LLR	0.04	1.91820392137009	1.89220635038762	1.94440936749118
+O. sativa	<0.001	LLR	0.04	5.6126018081428	5.47312028586688	5.75506648195356
+A. thaliana	0.001-0.01	dot product (layer 11)	0.04	1.68929266713781	1.65618259218014	1.72317170759557
+A. thaliana	<0.001	dot product (layer 11)	0.04	1.44413693068704	1.41596095430339	1.47302008628704
+O. sativa	0.001-0.01	dot product (layer 11)	0.04	1.69513445620973	1.67230582291661	1.71843982109143
+O. sativa	<0.001	dot product (layer 11)	0.04	9.37171459783246	9.16241491840208	9.58225258823019
+A. thaliana	0.001-0.01	dot product (layer 21)	0.04	1.40465822138623	1.37864500611508	1.43132087962387
+A. thaliana	<0.001	dot product (layer 21)	0.04	1.23966875937099	1.21678481649364	1.26305667797411
+O. sativa	0.001-0.01	dot product (layer 21)	0.04	2.14564327509633	2.11595213960973	2.17568555969694
+O. sativa	<0.001	dot product (layer 21)	0.04	15.7771632768255	15.4404182661035	16.1127607506724
+A. thaliana	0.001-0.01	dot product (layer 31)	0.04	1.68970602202741	1.65656419397682	1.72354087728623
+A. thaliana	<0.001	dot product (layer 31)	0.04	1.4272524708277	1.39933055339902	1.45589976926807
+O. sativa	0.001-0.01	dot product (layer 31)	0.04	2.02185205428639	1.99404889249427	2.05003831457693
+O. sativa	<0.001	dot product (layer 31)	0.04	14.103013152026	13.7959839841026	14.4206849906182
+A. thaliana	0.001-0.01	dot product (layer 40)	0.04	1.41151419272004	1.38516766948566	1.43851926985581
+A. thaliana	<0.001	dot product (layer 40)	0.04	1.28141305180484	1.25770846196954	1.30569232959464
+O. sativa	0.001-0.01	dot product (layer 40)	0.04	1.5323993499345	1.51170985308841	1.55341662474786
+O. sativa	<0.001	dot product (layer 40)	0.04	7.67235888730279	7.50054453816972	7.84789763530505
+A. thaliana	0.001-0.01	phyloP	0.04	2.09559046072165	2.04926222705136	2.14297829851504
+A. thaliana	<0.001	phyloP	0.04	2.65597257771655	2.59856518505137	2.71455042918031
+O. sativa	0.001-0.01	phyloP	0.04	1.61849694001289	1.59718709057015	1.64022211010842
+O. sativa	<0.001	phyloP	0.04	0.809640070836025	0.770858801812313	0.849977873871861
+A. thaliana	0.001-0.01	phastCons	0.04	1.49959502534535	1.46956502742744	1.5304817231368
+A. thaliana	<0.001	phastCons	0.04	1.86191818466513	1.82575539405743	1.89922251270897
+O. sativa	0.001-0.01	phastCons	0.04	1.18894579061163	1.17320992674221	1.20481962666039
+O. sativa	<0.001	phastCons	0.04	0.497687975591887	0.470022436905745	0.526638020784996
+A. thaliana	0.001-0.01	GPN	0.05	2.0758876934699	2.03457552451978	2.11813644025119
+A. thaliana	<0.001	GPN	0.05	2.45378999630138	2.40559517585373	2.50258697747763
+O. sativa	0.001-0.01	GPN	0.05	1.33965649735353	1.32365341301537	1.35588073728866
+O. sativa	<0.001	GPN	0.05	1.72239341553005	1.66984866708293	1.77628251646092
+A. thaliana	0.001-0.01	LLR	0.05	1.55174951268505	1.52423519992644	1.57981114088671
+A. thaliana	<0.001	LLR	0.05	1.64353107458719	1.61503824135057	1.67274276227319
+O. sativa	0.001-0.01	LLR	0.05	1.86505502746517	1.84237815026104	1.88792303369666
+O. sativa	<0.001	LLR	0.05	5.16830667123936	5.04829140247517	5.29009679827909
+A. thaliana	0.001-0.01	dot product (layer 11)	0.05	1.59604179849022	1.56839087637682	1.6241855531187
+A. thaliana	<0.001	dot product (layer 11)	0.05	1.37077087323515	1.34715187242273	1.39490465199656
+O. sativa	0.001-0.01	dot product (layer 11)	0.05	1.67019606864879	1.64996411535055	1.69084518716361
+O. sativa	<0.001	dot product (layer 11)	0.05	9.03968045100982	8.85533789602421	9.22595708585399
+A. thaliana	0.001-0.01	dot product (layer 21)	0.05	1.32808928192591	1.30633225760426	1.35034795183316
+A. thaliana	<0.001	dot product (layer 21)	0.05	1.17799120384187	1.15879316900197	1.19754156139607
+O. sativa	0.001-0.01	dot product (layer 21)	0.05	2.03055298953996	2.00541606594466	2.0558889696073
+O. sativa	<0.001	dot product (layer 21)	0.05	14.2222047152541	13.945790003853	14.5111520913723
+A. thaliana	0.001-0.01	dot product (layer 31)	0.05	1.56221644656392	1.53532057297579	1.58959466695536
+A. thaliana	<0.001	dot product (layer 31)	0.05	1.33598717162887	1.31310663793255	1.35939988676715
+O. sativa	0.001-0.01	dot product (layer 31)	0.05	1.94462136909251	1.92053155431956	1.96873495691104
+O. sativa	<0.001	dot product (layer 31)	0.05	13.1534116424103	12.901511252459	13.4294182875728
+A. thaliana	0.001-0.01	dot product (layer 40)	0.05	1.36554172684486	1.3428894794818	1.38871284475542
+A. thaliana	<0.001	dot product (layer 40)	0.05	1.24458469330099	1.22417107575019	1.26547594818397
+O. sativa	0.001-0.01	dot product (layer 40)	0.05	1.49661087599014	1.47849362689841	1.51507957530659
+O. sativa	<0.001	dot product (layer 40)	0.05	7.08364566252864	6.9341871461456	7.2323520729574
+A. thaliana	0.001-0.01	phyloP	0.05	2.04273414727479	2.00348672865142	2.0828553304385
+A. thaliana	<0.001	phyloP	0.05	2.56940568337409	2.52144163014719	2.61888439523929
+O. sativa	0.001-0.01	phyloP	0.05	1.5797117403782	1.56094039384276	1.59886017972503
+O. sativa	<0.001	phyloP	0.05	0.771601503997123	0.737689786190045	0.806734050365224
+A. thaliana	0.001-0.01	phastCons	0.05	1.41808098454463	1.39312363326123	1.44363889892379
+A. thaliana	<0.001	phastCons	0.05	1.74023030274344	1.71042922540453	1.77075390134839
+O. sativa	0.001-0.01	phastCons	0.05	1.17589476498483	1.16192048062619	1.19006515909256
+O. sativa	<0.001	phastCons	0.05	0.527300889034444	0.501721360293282	0.553823787798615

Figures/Fig7_panelc.txt

@@ -0,0 +1,81 @@
+Species	Label	Score	Cutoff	OR	ORLCI	ORUCI
+A. thaliana	coding	GPN	0.01	1.15149325913358	0.878023512815937	1.48525284063787
+A. thaliana	non-coding	GPN	0.01	1.6385209054985	1.33012851806986	1.99959201513652
+A. thaliana	coding	phyloP	0.01	1.23375497298719	0.992924643573568	1.51709251810142
+A. thaliana	non-coding	phyloP	0.01	1.19797829556504	0.943151741059582	1.5023232600968
+A. thaliana	coding	phastCons	0.01	1.11346862618412	0.845152159956271	1.44193122840763
+A. thaliana	non-coding	phastCons	0.01	1.10875981284169	0.865916260227574	1.40035275040863
+A. thaliana	coding	LLR	0.01	0.938439724304913	0.69528968070105	1.24086863428277
+A. thaliana	non-coding	LLR	0.01	1.7852347763965	1.46134959873797	2.16232755996585
+A. thaliana	coding	dot product (layer 11)	0.01	1.3505523443766	1.04860887463022	1.71475973571805
+A. thaliana	non-coding	dot product (layer 11)	0.01	2.88185751952188	2.43960361540078	3.3858252067243
+A. thaliana	coding	dot product (layer 21)	0.01	1.49487099395042	1.1780229375524	1.87343554202231
+A. thaliana	non-coding	dot product (layer 21)	0.01	1.37267107200458	1.08845447474317	1.71061081883935
+A. thaliana	coding	dot product (layer 31)	0.01	1.01684763530313	0.762128518233314	1.33130365245969
+A. thaliana	non-coding	dot product (layer 31)	0.01	2.28373175231466	1.90289468547401	2.72217762671585
+A. thaliana	coding	dot product (layer 40)	0.01	1.44607347278545	1.1343017341034	1.81971300792749
+A. thaliana	non-coding	dot product (layer 40)	0.01	2.8240591129705	2.39284501729866	3.3149035910378
+A. thaliana	coding	GPN	0.02	1.21863294420981	1.01369607088174	1.45416311111647
+A. thaliana	non-coding	GPN	0.02	1.59720416243324	1.37712422876677	1.84395066320483
+A. thaliana	coding	phyloP	0.02	1.2635062963944	1.0538902590977	1.50400368449058
+A. thaliana	non-coding	phyloP	0.02	1.21372106899637	1.02777237017571	1.42476647190925
+A. thaliana	coding	phastCons	0.02	1.22850298310606	1.02261532261873	1.46499003926591
+A. thaliana	non-coding	phastCons	0.02	1.17091896394563	0.989489356133552	1.3771033098622
+A. thaliana	coding	LLR	0.02	1.04251738140831	0.85509572650409	1.25985200644557
+A. thaliana	non-coding	LLR	0.02	1.70212466728269	1.47392820268947	1.95722353865806
+A. thaliana	coding	dot product (layer 11)	0.02	1.64831352642149	1.40284897895137	1.9261177841857
+A. thaliana	non-coding	dot product (layer 11)	0.02	2.78813280566878	2.47341838540928	3.13469019506542
+A. thaliana	coding	dot product (layer 21)	0.02	1.15764816647232	0.958833880485238	1.38685016652752
+A. thaliana	non-coding	dot product (layer 21)	0.02	2.00409805971712	1.74787672789581	2.28914763297693
+A. thaliana	coding	dot product (layer 31)	0.02	1.05490009311297	0.866027092636251	1.27389315783325
+A. thaliana	non-coding	dot product (layer 31)	0.02	2.16858987919223	1.90087664564012	2.46552472617563
+A. thaliana	coding	dot product (layer 40)	0.02	1.29064133237207	1.0786249104618	1.53356177192815
+A. thaliana	non-coding	dot product (layer 40)	0.02	2.46328543265941	2.17534329302053	2.78135213868627
+A. thaliana	coding	GPN	0.03	1.20282721985064	1.03426646674918	1.39208313884168
+A. thaliana	non-coding	GPN	0.03	1.48478186529501	1.30993585389488	1.67753026648217
+A. thaliana	coding	phyloP	0.03	1.24073327146706	1.06878554790175	1.43351097476107
+A. thaliana	non-coding	phyloP	0.03	1.21901039782217	1.06524648281977	1.38964488631166
+A. thaliana	coding	phastCons	0.03	1.22229866346993	1.05214718664718	1.41314866229905
+A. thaliana	non-coding	phastCons	0.03	1.08807283305442	0.943996132749947	1.24876305891899
+A. thaliana	coding	LLR	0.03	1.08380955478613	0.925130103269385	1.26286607688666
+A. thaliana	non-coding	LLR	0.03	1.60290654043459	1.42029078245583	1.80368905524625
+A. thaliana	coding	dot product (layer 11)	0.03	1.58866051995537	1.3893698686209	1.80987474248079
+A. thaliana	non-coding	dot product (layer 11)	0.03	2.58364001941363	2.33373912829111	2.8546752824397
+A. thaliana	coding	dot product (layer 21)	0.03	0.996133183461066	0.844720739907566	1.16773908243927
+A. thaliana	non-coding	dot product (layer 21)	0.03	2.06582308421483	1.84940310436603	2.30219444264047
+A. thaliana	coding	dot product (layer 31)	0.03	1.04237819254903	0.886910602335221	1.21809063213958
+A. thaliana	non-coding	dot product (layer 31)	0.03	2.11267804993853	1.8938651612622	2.35146388895535
+A. thaliana	coding	dot product (layer 40)	0.03	1.23930809668863	1.06756264031319	1.43182573656651
+A. thaliana	non-coding	dot product (layer 40)	0.03	2.35652015082284	2.12354592052939	2.6097999717561
+A. thaliana	coding	GPN	0.04	1.18038682595108	1.03432564539768	1.3421696499752
+A. thaliana	non-coding	GPN	0.04	1.48632945019287	1.33306314561803	1.65341906655882
+A. thaliana	coding	phyloP	0.04	1.18157887749402	1.03506374464616	1.34386708009336
+A. thaliana	non-coding	phyloP	0.04	1.2020562574825	1.06800687619484	1.34903810311453
+A. thaliana	coding	phastCons	0.04	1.18543281608856	1.03898158676034	1.34754190769936
+A. thaliana	non-coding	phastCons	0.04	1.08949071109693	0.963334600951261	1.22833487552266
+A. thaliana	coding	LLR	0.04	1.10438734809818	0.963966489676656	1.26032756215295
+A. thaliana	non-coding	LLR	0.04	1.49215345935172	1.3386820524722	1.65946746170896
+A. thaliana	coding	dot product (layer 11)	0.04	1.52884601775814	1.35794680998799	1.71645355289076
+A. thaliana	non-coding	dot product (layer 11)	0.04	2.50076655040727	2.28538865066211	2.73263339860938
+A. thaliana	coding	dot product (layer 21)	0.04	1.02927877318171	0.894300469142291	1.17967633185661
+A. thaliana	non-coding	dot product (layer 21)	0.04	2.1013878287509	1.90945063363795	2.30881165973883
+A. thaliana	coding	dot product (layer 31)	0.04	1.05026689969085	0.913578020723768	1.20233207351624
+A. thaliana	non-coding	dot product (layer 31)	0.04	2.05429535288686	1.86536569971145	2.25853318983591
+A. thaliana	coding	dot product (layer 40)	0.04	1.25213032338587	1.10082764733946	1.41932968876037
+A. thaliana	non-coding	dot product (layer 40)	0.04	2.18004895628444	1.98488755101312	2.39076095502702
+A. thaliana	coding	GPN	0.05	1.19774726995602	1.06475478199342	1.3435051587008
+A. thaliana	non-coding	GPN	0.05	1.44779988470034	1.31144357804664	1.59527389213163
+A. thaliana	coding	phyloP	0.05	1.18230976391146	1.05048714168907	1.32688410199608
+A. thaliana	non-coding	phyloP	0.05	1.15722841011739	1.03885310118241	1.28604376057543
+A. thaliana	coding	phastCons	0.05	1.15196773527778	1.0218984039543	1.2947674960409
+A. thaliana	non-coding	phastCons	0.05	1.00680796170396	0.897939057008922	1.12579652847575
+A. thaliana	coding	LLR	0.05	1.09779957717192	0.971497677119463	1.23669946360079
+A. thaliana	non-coding	LLR	0.05	1.41285418645614	1.27849002573493	1.55829469738091
+A. thaliana	coding	dot product (layer 11)	0.05	1.4654382367406	1.31477362943656	1.62976454971543
+A. thaliana	non-coding	dot product (layer 11)	0.05	2.33032243138904	2.14326813820111	2.53034555672067
+A. thaliana	coding	dot product (layer 21)	0.05	1.06832362573167	0.943865578075569	1.20528000265378
+A. thaliana	non-coding	dot product (layer 21)	0.05	2.11201860480956	1.93764146934321	2.29895005055324
+A. thaliana	coding	dot product (layer 31)	0.05	1.07035321979091	0.945650178709713	1.20753642170338
+A. thaliana	non-coding	dot product (layer 31)	0.05	2.01564146130028	1.84658881909769	2.19716444692717
+A. thaliana	coding	dot product (layer 40)	0.05	1.20591550009589	1.07218738488266	1.3525178012126
+A. thaliana	non-coding	dot product (layer 40)	0.05	2.07839222724193	1.90667420193793	2.26269204593029

Figures/Fig7_paneld.txt

@@ -0,0 +1,55 @@
+Model1	Model2	r	Layer
+GPN	GPN	NA	Loss-based
+phyloP	GPN	-0.20430223352512	Loss-based
+phastCons	GPN	-0.0988748514289571	Loss-based
+GPN	LLR	0.594225893848547	Loss-based
+phyloP	LLR	-0.133516632221117	Loss-based
+phastCons	LLR	-0.0358971601734904	Loss-based
+GPN	cos similarity	0.0573209639597964	11
+phyloP	cos similarity	0.00233138491226243	11
+phastCons	cos similarity	0.0248488140472222	11
+GPN	dot product	-0.0935924070591606	11
+phyloP	dot product	-0.115887001390502	11
+phastCons	dot product	-0.177584590910111	11
+GPN	l1 distance	-0.0778989339721649	11
+phyloP	l1 distance	0.00685386455309636	11
+phastCons	l1 distance	-0.0310017670716644	11
+GPN	l2 distance	-0.0830159041999567	11
+phyloP	l2 distance	0.00422985416066335	11
+phastCons	l2 distance	-0.0366067676484995	11
+GPN	cos similarity	0.0656942093351704	21
+phyloP	cos similarity	0.00678946387997435	21
+phastCons	cos similarity	0.0291039251133519	21
+GPN	dot product	-0.133552573268592	21
+phyloP	dot product	-0.0998713277683583	21
+phastCons	dot product	-0.135953571130837	21
+GPN	l1 distance	-0.102875558990518	21
+phyloP	l1 distance	-0.00893751608057503	21
+phastCons	l1 distance	-0.0481006669057204	21
+GPN	l2 distance	-0.103498931570725	21
+phyloP	l2 distance	-0.00921390539952009	21
+phastCons	l2 distance	-0.0501028937746948	21
+GPN	cos similarity	0.0358596116768626	31
+phyloP	cos similarity	-0.00228886948737331	31
+phastCons	cos similarity	0.0102150000652027	31
+GPN	dot product	-0.123673103793413	31
+phyloP	dot product	-0.0771467998085015	31
+phastCons	dot product	-0.101970126555535	31
+GPN	l1 distance	-0.0908150470593039	31
+phyloP	l1 distance	0.000297805618807892	31
+phastCons	l1 distance	-0.0259016534709807	31
+GPN	l2 distance	-0.0740172196305742	31
+phyloP	l2 distance	0.00229576468778455	31
+phastCons	l2 distance	-0.0225394945339547	31
+GPN	cos similarity	0.0491586785072186	40
+phyloP	cos similarity	0.00222711329754801	40
+phastCons	cos similarity	0.0238743510053775	40
+GPN	dot product	-0.0261837904102534	40
+phyloP	dot product	-0.0693059004207869	40
+phastCons	dot product	-0.127992271052942	40
+GPN	l1 distance	-0.0788263269630498	40
+phyloP	l1 distance	0.00246841658677939	40
+phastCons	l1 distance	-0.0304553887788611	40
+GPN	l2 distance	-0.0802090769456271	40
+phyloP	l2 distance	0.00189805646307345	40
+phastCons	l2 distance	-0.0318934924590018	40

Figures/Fig8_panela.txt

@@ -0,0 +1,770 @@
+FPR	TPR	cutoff	Species
+0	0	0.9993863	M. esculenta
+0	0.00253164556962025	0.9987588	M. esculenta
+0	0.00506329113924051	0.9969193	M. esculenta
+0	0.00759493670886076	0.99685484	M. esculenta
+0	0.010126582278481	0.99524176	M. esculenta
+0	0.0126582278481013	0.9951438	M. esculenta
+0	0.0151898734177215	0.99500954	M. esculenta
+0	0.0177215189873418	0.99432296	M. esculenta
+0	0.020253164556962	0.99403894	M. esculenta
+0	0.0227848101265823	0.9939257	M. esculenta
+0	0.0253164556962025	0.99155027	M. esculenta
+0	0.0278481012658228	0.99152064	M. esculenta
+0	0.030379746835443	0.9899673	M. esculenta
+0	0.0329113924050633	0.98917305	M. esculenta
+0	0.0354430379746835	0.98862815	M. esculenta
+0	0.0379746835443038	0.98820513	M. esculenta
+0	0.0405063291139241	0.987435	M. esculenta
+0	0.0430379746835443	0.9874179	M. esculenta
+0	0.0455696202531646	0.98722214	M. esculenta
+0	0.0481012658227848	0.98653	M. esculenta
+0	0.0506329113924051	0.98624355	M. esculenta
+0	0.0531645569620253	0.9861407	M. esculenta
+0	0.0556962025316456	0.985868	M. esculenta
+0	0.0582278481012658	0.9849381	M. esculenta
+0	0.0607594936708861	0.98467475	M. esculenta
+0	0.0632911392405063	0.98426706	M. esculenta
+0	0.0658227848101266	0.98390055	M. esculenta
+0	0.0683544303797468	0.98286813	M. esculenta
+0	0.0708860759493671	0.9822648	M. esculenta
+0	0.0734177215189873	0.9819119	M. esculenta
+0	0.0759493670886076	0.981721	M. esculenta
+0	0.0784810126582278	0.9813573	M. esculenta
+0	0.0810126582278481	0.97986245	M. esculenta
+0	0.0835443037974684	0.9795567	M. esculenta
+0.00268096514745308	0.0835443037974684	0.9790615	M. esculenta
+0.00268096514745308	0.0860759493670886	0.9789475	M. esculenta
+0.00268096514745308	0.0886075949367089	0.9787072	M. esculenta
+0.00268096514745308	0.0911392405063291	0.97859114	M. esculenta
+0.00268096514745308	0.0936708860759494	0.9781865	M. esculenta
+0.00268096514745308	0.0962025316455696	0.9779579	M. esculenta
+0.00536193029490617	0.0962025316455696	0.9770656	M. esculenta
+0.00536193029490617	0.0987341772151899	0.97597325	M. esculenta
+0.00536193029490617	0.10126582278481	0.9751472	M. esculenta
+0.00536193029490617	0.10379746835443	0.9750424	M. esculenta
+0.00536193029490617	0.106329113924051	0.9750097	M. esculenta
+0.00536193029490617	0.108860759493671	0.974787	M. esculenta
+0.00536193029490617	0.111392405063291	0.97434837	M. esculenta
+0.00536193029490617	0.113924050632911	0.9743128	M. esculenta
+0.00536193029490617	0.116455696202532	0.97326875	M. esculenta
+0.00536193029490617	0.118987341772152	0.97199327	M. esculenta
+0.00536193029490617	0.121518987341772	0.9715275	M. esculenta
+0.00536193029490617	0.124050632911392	0.9707381	M. esculenta
+0.00536193029490617	0.126582278481013	0.9703124	M. esculenta
+0.00536193029490617	0.129113924050633	0.9702023	M. esculenta
+0.00536193029490617	0.131645569620253	0.9700501	M. esculenta
+0.00536193029490617	0.134177215189873	0.9698841	M. esculenta
+0.00536193029490617	0.136708860759494	0.96957326	M. esculenta
+0.00536193029490617	0.139240506329114	0.9693652	M. esculenta
+0.00536193029490617	0.141772151898734	0.9693494	M. esculenta
+0.00536193029490617	0.144303797468354	0.969276	M. esculenta
+0.00536193029490617	0.146835443037975	0.9672984	M. esculenta
+0.00536193029490617	0.149367088607595	0.9666686	M. esculenta
+0.00536193029490617	0.151898734177215	0.9660681	M. esculenta
+0.00536193029490617	0.154430379746835	0.96594363	M. esculenta
+0.00536193029490617	0.156962025316456	0.9656844	M. esculenta
+0.00536193029490617	0.159493670886076	0.96534157	M. esculenta
+0.00536193029490617	0.162025316455696	0.9645039	M. esculenta
+0.00536193029490617	0.164556962025316	0.964413	M. esculenta
+0.00536193029490617	0.167088607594937	0.9638329	M. esculenta
+0.00536193029490617	0.169620253164557	0.96329933	M. esculenta
+0.00536193029490617	0.172151898734177	0.9612809	M. esculenta
+0.00536193029490617	0.174683544303797	0.96092594	M. esculenta
+0.00804289544235925	0.174683544303797	0.9608111	M. esculenta
+0.00804289544235925	0.177215189873418	0.9606031	M. esculenta
+0.00804289544235925	0.179746835443038	0.96054167	M. esculenta
+0.00804289544235925	0.182278481012658	0.96038866	M. esculenta
+0.00804289544235925	0.184810126582278	0.960182	M. esculenta
+0.0107238605898123	0.184810126582278	0.95928174	M. esculenta
+0.0107238605898123	0.187341772151899	0.9580579	M. esculenta
+0.0107238605898123	0.189873417721519	0.9573414	M. esculenta
+0.0107238605898123	0.192405063291139	0.9565803	M. esculenta
+0.0107238605898123	0.19493670886076	0.9557293	M. esculenta
+0.0107238605898123	0.19746835443038	0.955552	M. esculenta
+0.0107238605898123	0.2	0.95480466	M. esculenta
+0.0107238605898123	0.20253164556962	0.954645	M. esculenta
+0.0107238605898123	0.205063291139241	0.9543146	M. esculenta
+0.0107238605898123	0.207594936708861	0.9541371	M. esculenta
+0.0107238605898123	0.210126582278481	0.953622	M. esculenta
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+1	1	0.0006209013	M. esculenta

Figures/Fig8_panelb.txt

@@ -0,0 +1,1001 @@
+region_id	pos	idx	abs_log2FC
+Chromosome13:27346902-27347901	27347266	364	0.000224431952540817
+Chromosome07:25136427-25137426	25137108	681	0.000371491362162368
+Chromosome06:27252852-27253851	27253324	472	0.000408694241880174
+Chromosome04:7417702-7418701	7418158	456	0.00041563059799301
+Chromosome05:1777352-1778351	1778027	675	0.000462034789606079
+Chromosome17:24226877-24227876	24227529	652	0.000582742290819247
+Chromosome03:835502-836501	836183	681	0.000710808271973576
+Chromosome15:1201177-1202176	1201696	519	0.000836328239703928
+Chromosome10:20661602-20662601	20662259	657	0.0008567596059643
+Chromosome04:26351202-26352201	26351673	471	0.000899318886581076
+Chromosome17:24901627-24902626	24901947	320	0.000957464928798647
+Chromosome13:27844827-27845826	27845505	678	0.00104510687004629
+Chromosome09:21737727-21738726	21738135	408	0.00109418251969964
+Chromosome15:11363302-11364301	11363902	600	0.00121151802960585
+Chromosome06:1501252-1502251	1501722	470	0.00121771919095645
+Chromosome09:5571002-5572001	5571473	471	0.00125007121171645
+Chromosome11:20965902-20966901	20966575	673	0.0012805146335125
+Chromosome13:8695302-8696301	8695617	315	0.00134865293965378
+Chromosome11:27010252-27011251	27010867	615	0.00136977177425645
+Chromosome18:10597127-10598126	10597731	604	0.0014075335831907
+Chromosome16:22953302-22954301	22953988	686	0.00142382656045894
+Chromosome15:646677-647676	647257	580	0.0014459574239284
+Chromosome09:2068002-2069001	2068302	300	0.0014696502844392
+Chromosome14:16375227-16376226	16375779	552	0.00152585407757113
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+Chromosome01:30082702-30083701	30083095	393	0.00170748097647038
+Chromosome06:13926627-13927626	13927036	409	0.00176903029397992
+Chromosome18:1097852-1098851	1098274	422	0.00179268468568085
+Chromosome01:33698727-33699726	33699394	667	0.00184756494112953
+Chromosome11:26247277-26248276	26247897	620	0.00188229286488622
+Chromosome14:11550877-11551876	11551179	302	0.00188248284507715
+Chromosome02:10199177-10200176	10199804	627	0.00188527554617976
+Chromosome17:23449302-23450301	23449775	473	0.00193408807423037
+Chromosome17:24905377-24906376	24905796	419	0.00199895862092042
+Chromosome16:25564602-25565601	25565025	423	0.00201448217014422
+Chromosome06:735327-736326	735996	669	0.00204048526363295
+Chromosome01:22839552-22840551	22839963	411	0.0020444103312916
+Chromosome17:21513202-21514201	21513878	676	0.00207678288424065
+Chromosome07:19539877-19540876	19540208	331	0.00212330149655501
+Chromosome10:25237477-25238476	25238039	562	0.00217315737039042
+Chromosome01:30684002-30685001	30684698	696	0.00220883965035644
+Chromosome14:8887102-8888101	8887653	551	0.00221467215289117
+Chromosome04:25409702-25410701	25410286	584	0.00227547917332243
+Chromosome05:19085152-19086151	19085664	512	0.00232269398485917
+Chromosome08:1759402-1760401	1760011	609	0.00233842603199015
+Chromosome11:23112027-23113026	23112441	414	0.00235462955768253
+Chromosome07:11421577-11422576	11422194	617	0.00239493227866433
+Chromosome11:9111802-9112801	9112220	418	0.00239499825726286
+Chromosome01:23487377-23488376	23487975	598	0.00239662300526929
+Chromosome14:3754652-3755651	3755275	623	0.00239681080065495
+Chromosome08:22848377-22849376	22849061	684	0.00241255793814258
+Chromosome14:13530327-13531326	13530701	374	0.00241379446327965
+Chromosome04:27547777-27548776	27548333	556	0.00244021921177711
+Chromosome15:6236677-6237676	6237320	643	0.00248198384081035
+Chromosome05:3193452-3194451	3194031	579	0.00251583846328618
+Chromosome15:1711527-1712526	1712146	619	0.00253868237387453
+Chromosome17:16690902-16691901	16691257	355	0.00254585938855324
+Chromosome09:5291902-5292901	5292474	572	0.00255801323286179
+Chromosome02:3224177-3225176	3224501	324	0.00258719145018459
+Chromosome18:9213252-9214251	9213907	655	0.00259850187878781
+Chromosome05:5168202-5169201	5168672	470	0.00261541224608925
+Chromosome14:6657052-6658051	6657629	577	0.002666452610246
+Chromosome06:23361002-23362001	23361690	688	0.00269142861076821
+Chromosome06:10210677-10211676	10211260	583	0.00271408585072934
+Chromosome02:27633677-27634676	27634252	575	0.00272627489890761
+Chromosome14:6589402-6590401	6589931	529	0.00273952378040715
+Chromosome12:28493627-28494626	28494039	412	0.00281765833561584
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Figures/Fig8_panelc.txt

@@ -0,0 +1,1201 @@
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Figures/Fig8_paneld.txt

@@ -0,0 +1,1201 @@
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Figures/Fig8_panelf.txt

@@ -0,0 +1,1131 @@
+GeneNum	Observed	Predicted	Tissue
+LG15:4066726-4072725	4067642	917	0.00366798601956998
+LG13:23873942-23879941	23878974	5033	0.00606860526309119
+LG5:9327352-9333351	9328273	922	0.00647634102610091
+LG15:4073979-4079978	4074913	935	0.00703043245146121
+LG3:25385199-25391198	25390278	5080	0.00963483766260823
+LG12:30852223-30858222	30853386	1164	0.0104491124354988
+LG15:2760706-2766705	2761592	887	0.0111070433796172
+LG12:29370862-29376861	29371706	845	0.0115257981086141
+LG3:23954781-23960780	23955698	918	0.0115663338189089
+LG10:17938560-17944559	17943572	5013	0.0119125768177534
+LG7:25247003-25253002	25247893	891	0.0120307753797017
+LG11:2496401-2502400	2497331	931	0.0120624643009758
+LG7:3356919-3362918	3361992	5074	0.0121940881902629
+LG11:11084402-11090401	11089591	5190	0.0124618846302359
+LG14:12630765-12636764	12631647	883	0.0130611025583244
+LG1:2694086-2700085	2699211	5126	0.0130897057472945
+LG14:13445040-13451039	13445909	870	0.0132163822074625
+LG4:2831623-2837622	2832430	808	0.0132948337144361
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