
Supplemental Fig. 2E. Data for the top panel are as follows. Data were normalized against the sum of all 4 nucleotides in each sample and each category for the top panel, and the AU/GC ratios were calculated for the bottom panel. 

nt A C G T 
LIGR_1nt 35521 19771 39803 37195 
LIGR_2nt 38022 39461 53618 60501
LIGR_3nt 24234 26063 26322 24019
LIGR_4-10nt 180025 161748 190778 172789
SPLASH_GMA_1nt 266526 108042 191008 348180
SPLASH_GMA_2nt 575711 468861 180089 1028481
SPLASH_GMA_3nt 123393 111972 87013 210898
SPLASH_GMA_4-10nt 89404 155796 112455 152625
SPLASH_GMT_1nt 168707 61667 85070 183347
SPLASH_GMT_2nt 213092 168050 103587 300558
SPLASH_GMT_3nt 36057 37442 38255 37086
SPLASH_GMT_4-10nt 36151 91192 56375 51618
SPLASH_ESA_1nt 1346912 351936 381968 1346429
SPLASH_ESA_2nt 1604985 1263859 650274 2285148
SPLASH_ESA_3nt 694560 365740 368819 718726
SPLASH_ESA_4-10nt 646633 586192 469286 684905
COMRADES_1nt 56144 28407 53532 132331
COMRADES_2nt 75010 46439 60652 127473
COMRADES_3nt 17314 27482 26300 31675
COMRADES_4-10nt 37761 48155 52609 44452
PARIS_HEK_1nt 35521 19771 39803 37195
PARIS_HEK_2nt 38022 39461 53618 60501
PARIS_HEK_3nt 24234 26063 26322 24019
PARIS_HEK_4-10nt 180025 161748 190778 172789
PARIS_mES_1nt 38309 31880 23029 40026
PARIS_mES_2nt 46021 40362 38042 52351
PARIS_mES_3nt 30098 31514 31937 29304
PARIS_mES_4-10nt 213763 352354 370219 224772'


Supplemental Fig. 2F. Data for the 3 panels are listed as follows. Data were normalized against the sum of all 4 nucleotides in each sample and each category. 

Top panel: all alignments  
nt A C G T
LIGR_1nt 31262 28175 53711 68614
LIGR_2nt 93651 30179 47021 133455
LIGR>2nt 15182059 18040552 19940038 17477114
SPLASH_GMA_1nt 196206 151486 221817 465051
SPLASH_GMA_2nt 569913 360389 193571 1012773
SPLASH_GMA>2nt 102523818 247123587 258108611 111966534
SPLASH_GMT_1nt 73763 80722 107254 348753
SPLASH_GMT_2nt 175475 221243 121836 450099
SPLASH_GMT>2nt 357173498 521649015 564292632 404275392
SPLASH_ESA_1nt 620749 324183 550418 2662678
SPLASH_ESA_2nt 1171841 1436255 768237 3368136
SPLASH_ESA>2nt 536321580 552493698 635889127 650297680
COMRADES_1nt 45297 81875 61622 156544
COMRADES_2nt 69683 52987 66240 139606
COMRADES>2nt 189412481 193506225 235386349 163493291
PARIS_HEK_1nt  43795 25695 54035 49831
PARIS_HEK_2nt  38300 42276 63807 69115
PARIS_HEK>2nt  268261388 643473989 669235478 290008826
PARIS_mES_1nt  54686 71135 86637 85646
PARIS_mES_2nt  50252 120302 90621 129077
PARIS_mES>2nt  539399298 1187208968 1300987419 668499172

Middle panel: all but rRNA+Rfam   
#remove the 45S and Rfam collection from RfamhumanrnaMrna and RfammousernaMrna
nt A C G T
LIGR_1nt 15328 10963 21251 44703
LIGR_2nt 18658 15790 21971 44757
LIGR>2nt 13569946 13638547 15400993 15619918
SPLASH_GMA_1nt 9089 4747 4779 19135
SPLASH_GMA_2nt 11755 12860 6381 23260
SPLASH_GMA>2nt 3841515 3983888 4600265 4655848
SPLASH_GMT_1nt 52307 41266 65527 285899
SPLASH_GMT_2nt 115142 112776 85358 279567
SPLASH_GMT>2nt 250219320 243991765 275491884 285781803
SPLASH_ESA_1nt 539098 284145 465863 2441154
SPLASH_ESA_2nt 1101582 873320 701156 2698091
SPLASH_ESA>2nt 525718943 525346578 607647584 638597001
COMRADES_1nt 26257 13218 31978 115547
COMRADES_2nt 64147 27285 42927 109799
COMRADES>2nt 165072283 137738553 176355399 137675718
PARIS_HEK_1nt 5506 3450 4145 7633
PARIS_HEK_2nt 8042 5377 6295 12380
PARIS_HEK>2nt 27019867 24843992 24801463 27678583
PARIS_mES_1nt 23854 7859 11141 17222
PARIS_mES_2nt 19106 13071 18778 24827
PARIS_mES>2nt 29715867 39799774 41268780 32873822

Bottom panel: all but rRNAs.   
#remove alignments mapped to hs45S and mm45S. 
nt A C G T
LIGR_1nt 29477 20694 47338 63510
LIGR_2nt 90954 26198 41306 127550
LIGR>2nt 13666904 13780886 15542809 15725164
SPLASH_GMA_1nt 25537 7074 18061 70495
SPLASH_GMA_2nt 28609 16776 13556 53363
SPLASH_GMA>2nt 3952943 4011385 4635682 4727441
SPLASH_GMT_1nt 53322 41517 66791 288223
SPLASH_GMT_2nt 116563 113029 86096 281355
SPLASH_GMT>2nt 250236897 244005308 275509800 285793416
SPLASH_ESA_1nt 550301 287752 482039 2509570
SPLASH_ESA_2nt 1123106 878615 710179 2733913
SPLASH_ESA>2nt 525864774 525365133 607669694 638689783
COMRADES_1nt 26697 13310 32362 116750
COMRADES_2nt 64568 27430 43164 110498
COMRADES>2nt 165078075 137743462 176361500 137680597
PARIS_HEK_1nt 7430 4358 5135 9778
PARIS_HEK_2nt 10388 7077 8799 15130
PARIS_HEK>2nt 27785334 25844651 25854147 28370086
PARIS_mES_1nt 25028 8540 12473 18647
PARIS_mES_2nt 19900 14009 19833 26422
PARIS_mES>2nt 30112880 40364712 41876258 33262167
