diff --git a/covid_comp_alldginn.txt b/covid_comp_alldginn.txt
index edb2c48ca832108c183944592c225f824ef8bdda..92fbab0e85d4443dfb39e42bf4e8d532f6c22bb2 100644
--- a/covid_comp_alldginn.txt
+++ b/covid_comp_alldginn.txt
@@ -1,4 +1,4 @@
-"Gene.name" "File" "Name" "GeneSize" "dginn.primate_NbSpecies" "dginn.primate_omegaM0Bpp" "dginn.primate_omegaM0codeml" "dginn.primate_BUSTED" "dginn.primate_BUSTED.p.value" "dginn.primate_MEME.NbSites" "dginn.primate_MEME.PSS" "dginn.primate_BppM1M2" "dginn.primate_BppM1M2.p.value" "dginn.primate_BppM1M2.NbSites" "dginn.primate_BppM1M2.PSS" "dginn.primate_BppM7M8" "dginn.primate_BppM7M8.p.value" "dginn.primate_BppM7M8.NbSites" "dginn.primate_BppM7M8.PSS" "dginn.primate_codemlM1M2" "dginn.primate_codemlM1M2.p.value" "dginn.primate_codemlM1M2.NbSites" "dginn.primate_codemlM1M2.PSS" "dginn.primate_codemlM7M8" "dginn.primate_codemlM7M8.p.value" "dginn.primate_codemlM7M8.NbSites" "dginn.primate_codemlM7M8.PSS" "bats_File" "bats_Name" "bats_GeneSize" "bats_NbSpecies" "bats_omegaM0Bpp" "bats_omegaM0codeml" "bats_BUSTED" "bats_BUSTED_p.value" "bats_MEME_NbSites" "bats_MEME_PSS" "bats_BppM1M2" "bats_BppM1M2_p.value" "bats_BppM1M2_NbSites" "bats_BppM1M2_PSS" "bats_BppM7M8" "bats_BppM7M8_p.value" "bats_BppM7M8_NbSites" "bats_BppM7M8_PSS" "bats_codemlM1M2" "bats_codemlM1M2_p.value" "bats_codemlM1M2_NbSites" "bats_codemlM1M2_PSS" "bats_codemlM7M8" "bats_codemlM7M8_p.value" "bats_codemlM7M8_NbSites" "bats_codemlM7M8_PSS" "bats_Lucie.s.comments" "bats_Action.taken" "status"
+"Gene.name" "File" "Name" "GeneSize" "dginn-primate_NbSpecies" "dginn-primate_omegaM0Bpp" "dginn-primate_omegaM0codeml" "dginn-primate_BUSTED" "dginn-primate_BUSTED.p.value" "dginn-primate_MEME.NbSites" "dginn-primate_MEME.PSS" "dginn-primate_BppM1M2" "dginn-primate_BppM1M2.p.value" "dginn-primate_BppM1M2.NbSites" "dginn-primate_BppM1M2.PSS" "dginn-primate_BppM7M8" "dginn-primate_BppM7M8.p.value" "dginn-primate_BppM7M8.NbSites" "dginn-primate_BppM7M8.PSS" "dginn-primate_codemlM1M2" "dginn-primate_codemlM1M2.p.value" "dginn-primate_codemlM1M2.NbSites" "dginn-primate_codemlM1M2.PSS" "dginn-primate_codemlM7M8" "dginn-primate_codemlM7M8.p.value" "dginn-primate_codemlM7M8.NbSites" "dginn-primate_codemlM7M8.PSS" "bats_File" "bats_Name" "bats_GeneSize" "bats_NbSpecies" "bats_omegaM0Bpp" "bats_omegaM0codeml" "bats_BUSTED" "bats_BUSTED_p.value" "bats_MEME_NbSites" "bats_MEME_PSS" "bats_BppM1M2" "bats_BppM1M2_p.value" "bats_BppM1M2_NbSites" "bats_BppM1M2_PSS" "bats_BppM7M8" "bats_BppM7M8_p.value" "bats_BppM7M8_NbSites" "bats_BppM7M8_PSS" "bats_codemlM1M2" "bats_codemlM1M2_p.value" "bats_codemlM1M2_NbSites" "bats_codemlM1M2_PSS" "bats_codemlM7M8" "bats_codemlM7M8_p.value" "bats_codemlM7M8_NbSites" "bats_codemlM7M8_PSS" "bats_Lucie.s.comments" "bats_Action.taken" "status"
"1" "AAR2" "AAR2_sequences_filtered_longestORFs_mafft_mincov_prank" "AAR2_all" 601 24 "0.138510454262" "0.105" "N" "0.9333" 1 "264" "N" "0.9999992818091265" 0 "na" "N" "0.9999999748811209" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "AAR2_sequences_filtered_longestORFs_mafft_prank" "AAR2" 543 12 "0.111382448975" "0.103" "N" 1 0 "na" "N" "0.9999998011153564" 0 "na" "N" "0.0883931847285696" 0 "na" "N" "1.0" 0 "na" "N" "0.2574319154136435" 0 "na" "" "" "shared"
"2" "AASS" "AASS_sequences_filtered_longestORFs_mafft_mincov_prank" "AASS_all" 1460 24 "0.146308728224" "0.136" "N" "0.4684" 8 "345, 464, 840, 841, 1194, 1235, 1238, 1375" "N" "0.9999992149344861" 0 "na" "N" "0.9999999473147924" 0 "na" "N" "1.0" 0 "na" "N" "0.8344353586953767" 0 "na" "AASS_sequences_filtered_longestORFs_mafft_prank" "AASS" 1418 12 "0.168200575660" "0.165" "N" 0.0514 8 "44, 54, 65, 336, 360, 382, 384, 729" "N" "0.7898559819260855" 0 "na" "Y" "3.993698374833498e-08" 13 "41, 42, 54, 65, 165, 382, 545, 577, 642, 845, 906, 914, 921" "N" "0.3072787386016008" 0 "na" "Y" "0.00623236128209284" 0 "" "" "" "shared"
"3" "AATF" "AATF_sequences_filtered_longestORFs_mafft_mincov_prank" "AATF_all" 814 24 "0.272118991707" "0.273" "Y" "0.0000" 10 "7, 133, 236, 291, 307, 426, 548, 549, 602, 720" "N" "0.9999990153742446" 0 "na" "N" "0.999382674275042" 0 "na" "N" "1.0" 0 "na" "N" "0.2615839537910964" 0 "na" "AATF_sequences_filtered_longestORFs_mafft_prank" "AATF" 795 11 "0.212648396462" "0.208" "N" 0.9809 6 "136, 140, 162, 182, 449, 669" "N" "0.999998128316225" 0 "na" "N" "0.37817758541461555" 0 "na" "N" "1.0" 0 "na" "N" "0.8869204367172543" 0 "na" "" "" "shared"
@@ -422,36 +422,36 @@ But Genetic Innovation by splicing variants YES.
"407" "TMEM39B" "TMEM39B_sequences_filtered_longestORFs_mafft_mincov_prank" "TMEM39B_all" 1232 24 "0.031066125277" "0.042" "Y" "0.0000" 3 "51, 277, 300" "N" "0.999999462436025" 0 "na" "Y" "0.0012595106626096717" 2 "302, 512" "Y" "4.1185887075334635e-06" 3 "51, 176, 221" "Y" "5.997038937209627e-09" 5 "51, 176, 221, 276, 302" "TMEM39B_bat_same_mafft_prank" "TMEM39B" 880 12 "0.0272350070390354" "0.041" "Y" 0 3 "217, 331, 332" "N" "0.999999995285634" 0 "na" "N" "0.999708222630975" 0 "na" "Y" "1.5181774326767543e-06" 2 "169, 216" "na" "na" 0 "na" "" "" "shared"
"408" "TMEM97" "TMEM97_sequences_filtered_longestORFs_mafft_mincov_prank" "TMEM97_all" 1035 24 "0.167819929316" "0.322" "Y" "0.0000" 8 "392, 458, 796, 808, 873, 881, 882, 1033" "N" "0.9999997544607897" 0 "na" "N" "0.9999947415289641" 0 "na" "N" "1.0" 0 "na" "N" "0.9980019986669264" 0 "na" "TMEM97_sequences_filtered_longestORFs_mafft_prank" "TMEM97" 236 12 "0.420879156212" "0.471" "N" 0.9586 11 "5, 29, 31, 42, 104, 107, 120, 157, 179, 188, 205" "N" "0.7340928477677238" 0 "na" "N" "0.34471649535720056" 0 "na" "N" "0.31254713161813774" 0 "na" "N" "0.12681829056798818" 0 "na" "" "" "shared"
"409" "TMPRSS2" "TMPRSS2_sequences_filtered_longestORFs_mafft_mincov_prank" "TMPRSS2_all" 835 24 "0.309615659941" "0.303" "Y" "0.0000" 24 "202, 208, 210, 240, 252, 302, 307, 309, 341, 373, 391, 399, 440, 444, 453, 457, 505, 517, 692, 735, 751, 768, 789, 817" "N" "0.9999974339840445" 0 "na" "Y" "3.4286953818612497e-07" 4 "365, 453, 456, 680" "Y" "2.0991039390192704e-06" 4 "365, 453, 456, 680" "Y" "2.7365027702967978e-08" 6 "365, 453, 456, 680, 728, 768" "TMPRSS2_bat_same_mafft_prank" "TMPRSS2" 1174 12 "0.140290584008726" "0.145" "N" 0.9333 12 "630, 644, 649, 688, 775, 888, 921, 1003, 1051, 1055, 1066, 1173" "N" "0.999999010422051" 0 "na" "N" "0.621882294670985" 0 "na" "N" "1.0" 0 "na" "N" "0.788991288016829" 0 "na" "" "" "shared"
-"410" "TMPRSS2_cut" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "TMPRSS2_bat_select_cut_mafft_prank" "TMPRSS2" 574 12 "0.129489038364869" "0.127" "N" 0.9358 19 "59, 73, 78, 108, 115, 117, 121, 133, 144, 241, 259, 288, 321, 403, 421, 451, 455, 466, 573" "N" "0.999999906049202" 0 "na" "N" "0.334893426994811" 0 "na" "N" "1.0" 0 "na" "N" "0.4210515526274131" 0 "na" "" "" "onlybats"
-"411" "TOMM70" "TOMM70_sequences_filtered_longestORFs_mafft_mincov_prank" "TOMM70_all" 641 24 "0.059415639954" "0.054" "N" "1.0000" 0 "na" "N" "0.9875869801535943" 0 "na" "Y" "0.0343600371989326" 1 "62" "N" "0.8162782414252596" 0 "na" "N" "1.0" 0 "na" "TOMM70_sequences_filtered_longestORFs_mafft_prank" "TOMM70" 723 11 "0.029882210583" "0.030" "N" 1 0 "na" "N" "0.9999995844483192" 0 "na" "N" "0.9999999321098608" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "" "" "shared"
-"412" "TOR1A" "TOR1A_sequences_filtered_longestORFs_mafft_mincov_prank_part1_prank" "TOR1A_all_part1" 507 23 "0.099632009810" "0.101" "Y" "0.0196" 3 "56, 408, 486" "N" "0.8947941317286731" 0 "na" "N" "0.09775517975045724" 0 "na" "N" "0.74081822068192" 0 "na" "N" "0.055299025094692394" 0 "na" "TOR1A_sequences_filtered_longestORFs_duplication_remainingsequences_prank" "TOR1A_rem" 604 12 "0.066585977696" "0.080" "N" 0.5671 2 "121, 365" "N" "0.9999999594665504" 0 "na" "N" "0.9355750222791034" 0 "na" "N" "1.0" 0 "na" "Y" "0.02670244886475937" 0 "" "dupl ok" "" "shared"
-"413" "TOR1AIP1" "TOR1AIP1_sequences_filtered_longestORFs_mafft_mincov_prank" "TOR1AIP1_all" 1425 24 "0.577187484977" "0.581" "Y" "0.0005" 27 "144, 184, 187, 237, 239, 385, 409, 430, 457, 731, 734, 838, 848, 853, 857, 980, 1040, 1056, 1058, 1060, 1061, 1077, 1078, 1084, 1086, 1096, 1107" "Y" "1.2484315979276648e-11" 1 "1040" "Y" "2.502738548107742e-12" 2 "848, 1040" "Y" "1.7539158731449243e-10" 3 "848, 1040, 1182" "Y" "4.7170863106397096e-14" 5 "838, 848, 1040, 1093, 1182" "TOR1AIP1_sequences_filtered_longestORFs_mafft_prank" "TOR1AIP1" 743 12 "0.558329321702" "0.531" "Y" 0 0 "na" "Y" "0.0018966215330895428" 1 "509" "Y" "0.00023452293549997097" 2 "509, 515" "Y" "0.00014848895196983343" 2 "509, 515" "Y" "7.610360616693669e-06" 4 "317, 501, 509, 515" "PS yes" "" "shared"
-"414" "TOR1B" "TOR1A_sequences_filtered_longestORFs_mafft_mincov_prank_part2_prank" "TOR1A_all_part2" 862 22 "0.145576301068" "0.143" "N" "0.2796" 3 "46, 50, 79" "N" "0.9999997955924509" 0 "na" "N" "0.25516771425334167" 0 "na" "N" "1.0" 0 "na" "N" "0.28822899305718525" 0 "na" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "onlyprimates"
-"415" "TRIM59" "TRIM59_sequences_filtered_longestORFs_mafft_mincov_prank" "TRIM59_all" 2041 23 "0.306210926693" "0.294" "Y" "0.0010" 8 "522, 527, 555, 561, 607, 1946, 1997, 2022" "N" "0.22440658792179846" 0 "na" "Y" "0.029867764315102553" 2 "522, 562" "N" "0.2553806759881334" 0 "na" "Y" "0.031335614024921986" 0 "" "TRIM59_sequences_filtered_longestORFs_mafft_prank" "TRIM59" 439 12 "0.316982231988" "0.274" "N" 0.955 4 "239, 256, 354, 380" "N" "0.9999949480425412" 0 "na" "N" "0.05724083315647518" 0 "na" "N" "1.0" 0 "na" "N" "0.08492387601959336" 0 "na" "" "" "shared"
-"416" "TRMT1" "TRMT1_sequences_filtered_longestORFs_mafft_mincov_prank" "TRMT1_all" 1068 23 "0.221247278753" "0.201" "Y" "0.0002" 0 "na" "N" "0.9999999638539527" 0 "na" "Y" "0.004488704483443964" 4 "369, 969, 990, 1047" "N" "0.7025771933778344" 0 "na" "Y" "2.653621909059236e-05" 0 "" "TRMT1_sequences_filtered_longestORFs_mafft_prank" "TRMT1" 704 12 "0.212290337739" "0.192" "Y" 0 12 "2, 3, 24, 37, 54, 253, 254, 289, 324, 529, 652, 686" "N" "0.9999996975075649" 0 "na" "N" "0.526395175937924" 0 "na" "N" "1.0" 0 "na" "N" "0.9920319148372483" 0 "na" "" "" "shared"
-"417" "TUBGCP2" "TUBGCP2_sequences_filtered_longestORFs_mafft_mincov_prank" "TUBGCP2_all" 1664 24 "0.070451478024" "0.061" "Y" "0.0000" 5 "444, 445, 1331, 1463, 1613" "N" "0.9999999509855128" 0 "na" "Y" "0.00013629384562998488" 2 "238, 1550" "Y" "9.844623464290293e-05" 0 "" "Y" "0.0064608137605138396" 1 "238" "TUBGCP2_sequences_filtered_longestORFs_mafft_prank" "TUBGCP2" 1035 12 "0.055037331258" "0.044" "N" 0.8328 1 "954" "N" "0.9999999146402879" 0 "na" "N" "0.9999999871270121" 0 "na" "N" "1.0" 0 "na" "N" "0.9910403787728692" 0 "na" "" "" "shared"
-"418" "TUBGCP3" "TUBGCP3_sequences_filtered_longestORFs_mafft_mincov_prank" "TUBGCP3_all" 1850 24 "0.059328763974" "0.060" "Y" "0.0094" 8 "400, 668, 696, 781, 803, 1013, 1453, 1672" "N" "0.9999996171337266" 0 "na" "N" "0.6866955291166233" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "TUBGCP3_sequences_filtered_longestORFs_mafft_prank" "TUBGCP3" 1156 12 "0.073030126757" "0.072" "N" 1 2 "387, 430" "N" "0.33879849700735243" 0 "na" "Y" "1.2025913118475392e-07" 3 "387, 464, 490" "N" "0.5147880584569597" 0 "na" "Y" "0.018949078056685893" 1 "387" "" "" "shared"
-"419" "TYSND1" "TYSND1_sequences_filtered_longestORFs_mafft_mincov_prank" "TYSND1_all" 2653 21 "na" "na" "N" "0.8539" 9 "178, 192, 195, 255, 528, 532, 652, 1640, 2313" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "TYSND1_bat_select_mafft_prank" "TYSND1" 676 8 "0.21586721789783" "0.184" "N" 0.2118 5 "54, 93, 95, 124, 205" "N" "0.999998961509475" 0 "na" "Y" "0.00164138799933957" 1 "95" "N" "1.0" 0 "na" "Y" "1.0838402897292556e-06" 2 "95, 317" "" "" "shared"
-"420" "UBAP2" "UBAP2_sequences_filtered_longestORFs_mafft_mincov_prank" "UBAP2_all" 2044 24 "0.314627701475" "0.319" "N" "0.0883" 13 "569, 1183, 1189, 1271, 1390, 1449, 1457, 1584, 1656, 1668, 1673, 1674, 1861" "Y" "0.04356681576239805" 0 "" "Y" "0.00019803234787945596" 2 "570, 1664" "Y" "0.010224177708430196" 0 "" "Y" "6.585863546181317e-05" 0 "" "UBAP2_sequences_filtered_longestORFs_mafft_prank" "UBAP2" 1504 12 "0.237830734331" "0.242" "N" 1 0 "na" "N" "0.9999996078168666" 0 "na" "N" "0.9998839629323042" 0 "na" "N" "0.9980019986687417" 0 "na" "N" "1.0" 0 "na" "" "" "shared"
-"421" "UBAP2L" "UBAP2L_sequences_filtered_longestORFs_mafft_mincov_prank" "UBAP2L_all" 4315 24 "na" "na" "Y" "0.0000" 4 "113, 249, 484, 876" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "UBAP2L_sequences_filtered_longestORFs_mafft_prank" "UBAP2L" 3418 12 "na" "na" "Y" 0 3 "271, 476, 3110" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "could be cut at nt 5346 to reanalyze the 5-ter. Crashed because aln too long I think" "UBAP2L. Could not cut in the end. Many slice variants. Decided to keep whole and re-run. If too long, quit" "shared"
-"422" "UBXN8" "UBXN8_sequences_filtered_longestORFs_mafft_mincov_prank" "UBXN8_all" 699 23 "0.372707393059" "0.357" "Y" "0.0023" 8 "318, 405, 446, 473, 505, 509, 513, 627" "N" "0.9999984149270688" 0 "na" "N" "0.9999874088127017" 0 "na" "N" "1.0" 0 "na" "N" "0.9733612415242943" 0 "na" "UBXN8_sequences_filtered_longestORFs_mafft_prank" "UBXN8" 305 12 "0.404541986019" "0.393" "N" 1 1 "142" "N" "0.8595500425717232" 0 "na" "N" "0.570834465560978" 0 "na" "N" "0.8253068684916764" 0 "na" "N" "0.48772673462580574" 0 "na" "" "" "shared"
-"423" "UGGT2" "UGGT2_sequences_filtered_longestORFs_mafft_mincov_prank" "UGGT2_all" 2127 22 "0.368713980825" "0.315" "N" "0.6342" 19 "251, 252, 284, 310, 315, 355, 360, 399, 425, 453, 495, 509, 587, 764, 765, 1026, 1088, 1190, 1559" "Y" "0.020000998743095837" 47 "59, 316, 334, 392, 399, 417, 425, 462, 495, 496, 509, 580, 582, 595, 628, 633, 672, 683, 697, 706, 707, 764, 769, 801, 836, 839, 843, 899, 917, 936, 964, 988, 995, 998, 1018, 1044, 1088, 1114, 1190, 1203, 1212, 1230, 1330, 1345, 1348, 1358, 1363" "Y" "0.0007007729591462683" 14 "334, 509, 582, 672, 697, 764, 769, 964, 988, 1044, 1114, 1190, 1330, 1345" "Y" "0.00892409818605493" 0 "" "Y" "3.4209745443492555e-05" 3 "697, 1044, 1190" "UGGT2_sequences_filtered_longestORFs_mafft_prank" "UGGT2" 1721 12 "0.271849324024" "0.248" "Y" 0.015 15 "154, 156, 623, 677, 691, 738, 780, 876, 915, 932, 1051, 1174, 1301, 1329, 1349" "N" "0.9999994895407719" 0 "na" "N" "0.4009484925650369" 0 "na" "N" "1.0" 0 "na" "N" "0.3686159363035691" 0 "na" "" "" "shared"
-"424" "UPF1" "UPF1_sequences_filtered_longestORFs_mafft_mincov_prank" "UPF1_all" 1740 24 "na" "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "UPF1_sequences_filtered_longestORFs_mafft_prank" "UPF1" 1268 12 "0.005967468791" "0.004" "N" 1 0 "na" "N" "0.9999999999008651" 0 "na" "N" "0.9999900181399214" 0 "na" "N" "0.9940179640545284" 0 "na" "N" "0.9940179640545284" 0 "na" "" "" "shared"
-"425" "USP13" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "USP13_sequences_filtered_longestORFs_mafft_prank" "USP13" 957 12 "0.037174112882" "0.037" "N" 1 2 "374, 873" "N" "0.9999987827948775" 0 "na" "Y" "0.0190013570231371" 2 "586, 706" "N" "1.0" 0 "na" "N" "0.99900049983408" 0 "na" "" "" "onlybats"
-"426" "USP54" "USP54_sequences_filtered_longestORFs_mafft_mincov_prank" "USP54_all" 2486 24 "0.386068465868" "0.385" "N" "0.6967" 22 "464, 1198, 1478, 1525, 1562, 1591, 1627, 1635, 1688, 1712, 1765, 1784, 1862, 1875, 1988, 1989, 1996, 2118, 2234, 2341, 2347, 2410" "Y" "4.585969349940591e-12" 2 "1478, 2234" "Y" "1.025159258712707e-12" 2 "1478, 2234" "Y" "6.791054347170535e-13" 2 "1478, 2234" "na" "na" 0 "na" "USP54_sequences_filtered_longestORFs_mafft_prank" "USP54" 2053 11 "0.366806019369" "0.362" "Y" 0.0301 11 "845, 1129, 1160, 1290, 1291, 1405, 1412, 1732, 1823, 1939, 1985" "N" "0.9997345689145414" 0 "na" "N" "0.15291027386116157" 0 "na" "N" "0.5927396589958697" 0 "na" "N" "0.31192266203294183" 0 "na" "" "" "shared"
-"427" "VPS11" "VPS11_sequences_filtered_longestORFs_mafft_mincov_prank" "VPS11_all" 1500 24 "0.048270606305" "0.042" "N" "0.5166" 5 "440, 528, 682, 787, 854" "N" "0.9999985946152136" 0 "na" "Y" "0.0008361633364003558" 3 "789, 854, 1373" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "VPS11_sequences_filtered_longestORFs_mafft_prank" "VPS11" 1166 12 "0.078603582166" "0.072" "N" 0.0824 5 "27, 304, 314, 591, 596" "N" "0.9999993365374775" 0 "na" "Y" "0.012111394464395" 4 "21, 63, 342, 596" "N" "1.0" 0 "na" "N" "0.5117085777865054" 0 "na" "" "" "shared"
-"428" "VPS39" "VPS39_sequences_filtered_longestORFs_mafft_mincov_prank" "VPS39_all" 1501 23 "0.046946875948" "0.052" "Y" "0.0000" 6 "68, 135, 146, 169, 225, 706" "Y" "7.272055658525019e-16" 1 "146" "Y" "2.5399423605918594e-30" 1 "146" "Y" "2.7057022431548876e-16" 1 "146" "Y" "1.5006105308565566e-22" 1 "146" "VPS39_sequences_filtered_longestORFs_mafft_prank" "VPS39" 1042 12 "0.056596878456" "0.060" "Y" 0 4 "79, 115, 930, 933" "Y" "0.0036263867910577537" 1 "115" "Y" "3.2872363224224216e-11" 3 "115, 464, 723" "Y" "0.002538961855010523" 1 "115" "Y" "1.5934882242290877e-05" 1 "115" "position 115 due to internal splice variant" "" "shared"
-"429" "WASHC4" "WASHC4_sequences_filtered_longestORFs_mafft_mincov_prank" "WASHC4_all" 1602 23 "0.054671143559" "0.054" "Y" "0.0000" 32 "191, 361, 416, 453, 483, 510, 541, 571, 577, 602, 606, 763, 798, 802, 909, 818, 846, 850, 885, 891, 941, 1013, 1027, 1077, 1185, 1211, 1220, 1404, 1432, 1439, 1445, 1447" "N" "0.9934604233737435" 0 "na" "Y" "0.00020410173498656788" 3 "891, 1447, 1448" "N" "0.835270211411029" 0 "na" "N" "0.18787094775098143" 0 "na" "WASHC4_sequences_filtered_longestORFs_mafft_prank" "WASHC4" 1291 12 "0.047673831087" "0.043" "Y" 2e-04 1 "37" "N" "0.9999992783153051" 0 "na" "Y" "9.046577638308179e-07" 16 "37, 242, 245, 389, 506, 578, 630, 1073, 1084, 1152, 1176, 1207, 1208, 1267, 1275, 1278" "N" "0.9990004998331715" 0 "na" "N" "0.5127330190420621" 0 "na" "" "" "shared"
-"430" "WFS1" "WFS1_sequences_filtered_longestORFs_mafft_mincov_prank" "WFS1_all" 1072 24 "0.081575261516" "0.056" "N" "0.2613" 6 "78, 118, 486, 768, 806, 1004" "N" "0.9999996897186547" 0 "na" "Y" "9.570229689317189e-07" 5 "101, 118, 125, 230, 772" "N" "0.39971639333834935" 0 "na" "Y" "2.184769995878869e-06" 2 "118, 230" "WFS1_sequences_filtered_longestORFs_mafft_prank" "WFS1" 1109 11 "0.115587068116" "0.087" "Y" 0.0287 10 "166, 217, 483, 542, 647, 749, 768, 790, 888, 893" "N" "0.9999992486685281" 0 "na" "Y" "0.03804197055110089" 1 "166" "N" "1.0" 0 "na" "N" "0.5449833692075639" 0 "na" "" "" "shared"
-"431" "WFS1[0-2346]" "WFS1_sequences_filtered_longestORFs_mafft_mincov_prank_frag0to2346" "WFS1_all[0-2346]" 782 24 "0.110155273852" "0.078" "N" "0.4926" 5 "69, 118, 374, 486, 768" "N" "0.9999999833444236" 0 "na" "Y" "2.573536088277023e-05" 5 "101, 118, 125, 230, 772" "N" "1.0" 0 "na" "Y" "8.36043582541349e-06" 2 "118, 230" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "onlyprimates"
-"432" "WFS1[2345-3216]" "WFS1_sequences_filtered_longestORFs_mafft_mincov_prank_frag2345to3216" "WFS1_all[2345-3216]" 290 24 "0.021378658292" "0.016" "N" "0.5279" 2 "24, 222" "N" "0.9999999893580026" 0 "na" "N" "0.9312768299514572" 0 "na" "N" "1.0" 0 "na" "N" "0.9990004998331715" 0 "na" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "onlyprimates"
-"433" "YIF1A" "YIF1A_sequences_filtered_longestORFs_mafft_mincov_prank_part1_prank" "YIF1A_all_part1" 1223 24 "0.122099669920" "0.108" "N" "1.0000" 1 "190" "N" "0.9999998503785831" 0 "na" "N" "0.9986341687072853" 0 "na" "N" "0.7276027884144418" 0 "na" "N" "0.2608003778811103" 0 "na" "YIF1A_sequences_filtered_longestORFs_mafft_prank_part2_prank" "YIF1A_part2" 307 12 "0.092980087519" "0.083" "N" 1 0 "na" "N" "0.9999994430788052" 0 "na" "N" "0.9999999928145371" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "dupl yes" "" "shared"
-"434" "YIF1B" "YIF1A_sequences_filtered_longestORFs_mafft_mincov_prank_part2_prank" "YIF1A_all_part2" 682 11 "0.052814080269" "0.068" "N" "0.3729" 0 "na" "N" "0.9999997896859661" 0 "na" "N" "0.7552477206523797" 0 "na" "N" "0.34472785476720136" 0 "na" "N" "0.7641432556483685" 0 "na" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "onlyprimates"
-"435" "ZC3H18" "ZC3H18_sequences_filtered_longestORFs_mafft_mincov_prank" "ZC3H18_all" 1100 24 "0.087671644891" "0.083" "N" "0.6012" 3 "722, 782, 981" "N" "0.9999993848816375" 0 "na" "Y" "0.015299480271226013" 0 "" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "ZC3H18_sequences_filtered_longestORFs_mafft_prank" "ZC3H18" 1226 11 "0.200106682861" "0.187" "Y" 0.0016 4 "54, 654, 771, 1080" "N" "0.9999991996195169" 0 "na" "N" "0.5258352764131282" 0 "na" "N" "1.0" 0 "na" "N" "0.05596661089965757" 0 "na" "" "" "shared"
-"436" "ZC3H18[0-1101]" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "ZC3H18_sequences_filtered_longestORFs_mafft_prank_frag0to1101" "ZC3H18[0-1101]" 367 11 "0.229802082341" "0.219" "Y" 0.0191 3 "54, 148, 163" "N" "0.9999990616263259" 0 "na" "N" "0.24086994381226873" 0 "na" "Y" "0.0005745060096894928" 1 "188" "Y" "0.00030751090743914297" 1 "188" "" "" "onlybats"
-"437" "ZC3H18[1100-3678]" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "ZC3H18_sequences_filtered_longestORFs_mafft_prank_frag1100to3678" "ZC3H18[1100-3678]" 859 11 "0.204731954234" "0.189" "N" 0.7392 4 "287, 404, 713, 744" "N" "0.9999982891136908" 0 "na" "N" "0.781377329393951" 0 "na" "N" "1.0" 0 "na" "N" "0.46301306831102595" 0 "na" "" "" "onlybats"
-"438" "ZC3H7A" "ZC3H7A_sequences_filtered_longestORFs_mafft_mincov_prank" "ZC3H7A_all" 1242 24 "0.100883053669" "0.091" "Y" "0.0003" 8 "35, 150, 272, 389, 423, 540, 614, 1033" "N" "0.9999988073966796" 0 "na" "N" "0.9433840075471273" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "ZC3H7A_sequences_filtered_longestORFs_mafft_prank" "ZC3H7A" 1018 12 "0.207349246144" "0.173" "N" 0.9537 6 "194, 313, 318, 464, 606, 884" "N" "0.9999992934629285" 0 "na" "Y" "0.04687509899081552" 6 "92, 183, 216, 299, 318, 464" "N" "0.9314618921276734" 0 "na" "N" "0.3305491224578773" 0 "na" "" "" "shared"
-"439" "ZDHHC5" "ZDHHC5_sequences_filtered_longestORFs_mafft_mincov_prank" "ZDHHC5_all" 823 24 "0.078488206473" "0.075" "Y" "0.0351" 2 "597, 742" "N" "0.9848981471344455" 0 "na" "Y" "0.013502502486699652" 2 "404, 597" "N" "1.0" 0 "na" "N" "0.49213608756256844" 0 "na" "ZDHHC5_sequences_filtered_longestORFs_mafft_prank" "ZDHHC5" 768 12 "0.080123114130" "0.080" "N" 1 1 "95" "N" "0.8751057533143412" 0 "na" "Y" "0.00028950851490339055" 3 "95, 387, 688" "N" "1.0" 0 "na" "N" "0.26820598310847715" 0 "na" "" "" "shared"
-"440" "ZNF318" "ZNF318_sequences_filtered_longestORFs_mafft_mincov_prank" "ZNF318_all" 2496 24 "0.335852925463" "0.343" "Y" "0.0000" 32 "38, 75, 78, 104, 174, 392, 443, 703, 799, 1177, 1372, 1492, 1636, 1646, 1647, 1663, 1814, 1897, 1929, 1946, 1995, 2088, 2098, 2166, 2181, 2243, 2249, 2250, 2287, 2356, 2372, 2483" "Y" "0.0010039629225922107" 0 "" "Y" "1.3246467997073662e-05" 2 "1636, 2098" "Y" "7.829709942783089e-05" 2 "1636, 2098" "Y" "1.1348614329410036e-06" 6 "1636, 1817, 1929, 1954, 2098, 2243" "ZNF318_sequences_filtered_longestORFs_mafft_prank" "ZNF318" 2395 11 "0.361499795329" "0.353" "N" 0.1184 0 "na" "N" "0.8750270725798085" 0 "na" "N" "0.5452621832627409" 0 "na" "N" "0.6505090947231271" 0 "na" "N" "0.11567161588366141" 0 "na" "" "" "shared"
-"441" "ZNF503" "ZNF503_sequences_filtered_longestORFs_mafft_mincov_prank" "ZNF503_all" 802 21 "0.049882463869" "0.026" "N" "1.0000" 1 "87" "N" "0.9999980745506383" 0 "na" "Y" "0.024559140884415645" 1 "177" "N" "1.0" 0 "na" "N" "0.6206425292935231" 0 "na" "ZNF503_sequences_filtered_longestORFs_mafft_prank" "ZNF503" 682 9 "0.036470300914" "0.033" "N" 1 0 "na" "N" "0.9999987418249204" 0 "na" "N" "0.7780311233967817" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "" "" "shared"
-"442" "ZYG11B" "ZYG11B_sequences_filtered_longestORFs_mafft_mincov_prank" "ZYG11B_all" 1128 24 "0.023655415579" "0.025" "Y" "0.0000" 1 "998" "N" "0.9999975270769591" 0 "na" "Y" "0.020268109682591493" 4 "896, 990, 993, 998" "N" "1.0" 0 "na" "N" "0.6757041139607441" 0 "na" "ZYG11B_sequences_filtered_longestORFs_mafft_prank" "ZYG11B" 854 12 "0.019630434764" "0.021" "N" 1 0 "na" "N" "0.9999984077343413" 0 "na" "N" "0.1157682212961436" 0 "na" "N" "1.0" 0 "na" "N" "0.6750287475861135" 0 "na" "" "" "shared"
+"410" "TOMM70" "TOMM70_sequences_filtered_longestORFs_mafft_mincov_prank" "TOMM70_all" 641 24 "0.059415639954" "0.054" "N" "1.0000" 0 "na" "N" "0.9875869801535943" 0 "na" "Y" "0.0343600371989326" 1 "62" "N" "0.8162782414252596" 0 "na" "N" "1.0" 0 "na" "TOMM70_sequences_filtered_longestORFs_mafft_prank" "TOMM70" 723 11 "0.029882210583" "0.030" "N" 1 0 "na" "N" "0.9999995844483192" 0 "na" "N" "0.9999999321098608" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "" "" "shared"
+"411" "TOR1A" "TOR1A_sequences_filtered_longestORFs_mafft_mincov_prank_part1_prank" "TOR1A_all_part1" 507 23 "0.099632009810" "0.101" "Y" "0.0196" 3 "56, 408, 486" "N" "0.8947941317286731" 0 "na" "N" "0.09775517975045724" 0 "na" "N" "0.74081822068192" 0 "na" "N" "0.055299025094692394" 0 "na" "TOR1A_sequences_filtered_longestORFs_duplication_remainingsequences_prank" "TOR1A_rem" 604 12 "0.066585977696" "0.080" "N" 0.5671 2 "121, 365" "N" "0.9999999594665504" 0 "na" "N" "0.9355750222791034" 0 "na" "N" "1.0" 0 "na" "Y" "0.02670244886475937" 0 "" "dupl ok" "" "shared"
+"412" "TOR1AIP1" "TOR1AIP1_sequences_filtered_longestORFs_mafft_mincov_prank" "TOR1AIP1_all" 1425 24 "0.577187484977" "0.581" "Y" "0.0005" 27 "144, 184, 187, 237, 239, 385, 409, 430, 457, 731, 734, 838, 848, 853, 857, 980, 1040, 1056, 1058, 1060, 1061, 1077, 1078, 1084, 1086, 1096, 1107" "Y" "1.2484315979276648e-11" 1 "1040" "Y" "2.502738548107742e-12" 2 "848, 1040" "Y" "1.7539158731449243e-10" 3 "848, 1040, 1182" "Y" "4.7170863106397096e-14" 5 "838, 848, 1040, 1093, 1182" "TOR1AIP1_sequences_filtered_longestORFs_mafft_prank" "TOR1AIP1" 743 12 "0.558329321702" "0.531" "Y" 0 0 "na" "Y" "0.0018966215330895428" 1 "509" "Y" "0.00023452293549997097" 2 "509, 515" "Y" "0.00014848895196983343" 2 "509, 515" "Y" "7.610360616693669e-06" 4 "317, 501, 509, 515" "PS yes" "" "shared"
+"413" "TOR1B" "TOR1A_sequences_filtered_longestORFs_mafft_mincov_prank_part2_prank" "TOR1A_all_part2" 862 22 "0.145576301068" "0.143" "N" "0.2796" 3 "46, 50, 79" "N" "0.9999997955924509" 0 "na" "N" "0.25516771425334167" 0 "na" "N" "1.0" 0 "na" "N" "0.28822899305718525" 0 "na" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "onlyprimates"
+"414" "TRIM59" "TRIM59_sequences_filtered_longestORFs_mafft_mincov_prank" "TRIM59_all" 2041 23 "0.306210926693" "0.294" "Y" "0.0010" 8 "522, 527, 555, 561, 607, 1946, 1997, 2022" "N" "0.22440658792179846" 0 "na" "Y" "0.029867764315102553" 2 "522, 562" "N" "0.2553806759881334" 0 "na" "Y" "0.031335614024921986" 0 "" "TRIM59_sequences_filtered_longestORFs_mafft_prank" "TRIM59" 439 12 "0.316982231988" "0.274" "N" 0.955 4 "239, 256, 354, 380" "N" "0.9999949480425412" 0 "na" "N" "0.05724083315647518" 0 "na" "N" "1.0" 0 "na" "N" "0.08492387601959336" 0 "na" "" "" "shared"
+"415" "TRMT1" "TRMT1_sequences_filtered_longestORFs_mafft_mincov_prank" "TRMT1_all" 1068 23 "0.221247278753" "0.201" "Y" "0.0002" 0 "na" "N" "0.9999999638539527" 0 "na" "Y" "0.004488704483443964" 4 "369, 969, 990, 1047" "N" "0.7025771933778344" 0 "na" "Y" "2.653621909059236e-05" 0 "" "TRMT1_sequences_filtered_longestORFs_mafft_prank" "TRMT1" 704 12 "0.212290337739" "0.192" "Y" 0 12 "2, 3, 24, 37, 54, 253, 254, 289, 324, 529, 652, 686" "N" "0.9999996975075649" 0 "na" "N" "0.526395175937924" 0 "na" "N" "1.0" 0 "na" "N" "0.9920319148372483" 0 "na" "" "" "shared"
+"416" "TUBGCP2" "TUBGCP2_sequences_filtered_longestORFs_mafft_mincov_prank" "TUBGCP2_all" 1664 24 "0.070451478024" "0.061" "Y" "0.0000" 5 "444, 445, 1331, 1463, 1613" "N" "0.9999999509855128" 0 "na" "Y" "0.00013629384562998488" 2 "238, 1550" "Y" "9.844623464290293e-05" 0 "" "Y" "0.0064608137605138396" 1 "238" "TUBGCP2_sequences_filtered_longestORFs_mafft_prank" "TUBGCP2" 1035 12 "0.055037331258" "0.044" "N" 0.8328 1 "954" "N" "0.9999999146402879" 0 "na" "N" "0.9999999871270121" 0 "na" "N" "1.0" 0 "na" "N" "0.9910403787728692" 0 "na" "" "" "shared"
+"417" "TUBGCP3" "TUBGCP3_sequences_filtered_longestORFs_mafft_mincov_prank" "TUBGCP3_all" 1850 24 "0.059328763974" "0.060" "Y" "0.0094" 8 "400, 668, 696, 781, 803, 1013, 1453, 1672" "N" "0.9999996171337266" 0 "na" "N" "0.6866955291166233" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "TUBGCP3_sequences_filtered_longestORFs_mafft_prank" "TUBGCP3" 1156 12 "0.073030126757" "0.072" "N" 1 2 "387, 430" "N" "0.33879849700735243" 0 "na" "Y" "1.2025913118475392e-07" 3 "387, 464, 490" "N" "0.5147880584569597" 0 "na" "Y" "0.018949078056685893" 1 "387" "" "" "shared"
+"418" "TYSND1" "TYSND1_sequences_filtered_longestORFs_mafft_mincov_prank" "TYSND1_all" 2653 21 "na" "na" "N" "0.8539" 9 "178, 192, 195, 255, 528, 532, 652, 1640, 2313" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "TYSND1_bat_select_mafft_prank" "TYSND1" 676 8 "0.21586721789783" "0.184" "N" 0.2118 5 "54, 93, 95, 124, 205" "N" "0.999998961509475" 0 "na" "Y" "0.00164138799933957" 1 "95" "N" "1.0" 0 "na" "Y" "1.0838402897292556e-06" 2 "95, 317" "" "" "shared"
+"419" "UBAP2" "UBAP2_sequences_filtered_longestORFs_mafft_mincov_prank" "UBAP2_all" 2044 24 "0.314627701475" "0.319" "N" "0.0883" 13 "569, 1183, 1189, 1271, 1390, 1449, 1457, 1584, 1656, 1668, 1673, 1674, 1861" "Y" "0.04356681576239805" 0 "" "Y" "0.00019803234787945596" 2 "570, 1664" "Y" "0.010224177708430196" 0 "" "Y" "6.585863546181317e-05" 0 "" "UBAP2_sequences_filtered_longestORFs_mafft_prank" "UBAP2" 1504 12 "0.237830734331" "0.242" "N" 1 0 "na" "N" "0.9999996078168666" 0 "na" "N" "0.9998839629323042" 0 "na" "N" "0.9980019986687417" 0 "na" "N" "1.0" 0 "na" "" "" "shared"
+"420" "UBAP2L" "UBAP2L_sequences_filtered_longestORFs_mafft_mincov_prank" "UBAP2L_all" 4315 24 "na" "na" "Y" "0.0000" 4 "113, 249, 484, 876" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "UBAP2L_sequences_filtered_longestORFs_mafft_prank" "UBAP2L" 3418 12 "na" "na" "Y" 0 3 "271, 476, 3110" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "could be cut at nt 5346 to reanalyze the 5-ter. Crashed because aln too long I think" "UBAP2L. Could not cut in the end. Many slice variants. Decided to keep whole and re-run. If too long, quit" "shared"
+"421" "UBXN8" "UBXN8_sequences_filtered_longestORFs_mafft_mincov_prank" "UBXN8_all" 699 23 "0.372707393059" "0.357" "Y" "0.0023" 8 "318, 405, 446, 473, 505, 509, 513, 627" "N" "0.9999984149270688" 0 "na" "N" "0.9999874088127017" 0 "na" "N" "1.0" 0 "na" "N" "0.9733612415242943" 0 "na" "UBXN8_sequences_filtered_longestORFs_mafft_prank" "UBXN8" 305 12 "0.404541986019" "0.393" "N" 1 1 "142" "N" "0.8595500425717232" 0 "na" "N" "0.570834465560978" 0 "na" "N" "0.8253068684916764" 0 "na" "N" "0.48772673462580574" 0 "na" "" "" "shared"
+"422" "UGGT2" "UGGT2_sequences_filtered_longestORFs_mafft_mincov_prank" "UGGT2_all" 2127 22 "0.368713980825" "0.315" "N" "0.6342" 19 "251, 252, 284, 310, 315, 355, 360, 399, 425, 453, 495, 509, 587, 764, 765, 1026, 1088, 1190, 1559" "Y" "0.020000998743095837" 47 "59, 316, 334, 392, 399, 417, 425, 462, 495, 496, 509, 580, 582, 595, 628, 633, 672, 683, 697, 706, 707, 764, 769, 801, 836, 839, 843, 899, 917, 936, 964, 988, 995, 998, 1018, 1044, 1088, 1114, 1190, 1203, 1212, 1230, 1330, 1345, 1348, 1358, 1363" "Y" "0.0007007729591462683" 14 "334, 509, 582, 672, 697, 764, 769, 964, 988, 1044, 1114, 1190, 1330, 1345" "Y" "0.00892409818605493" 0 "" "Y" "3.4209745443492555e-05" 3 "697, 1044, 1190" "UGGT2_sequences_filtered_longestORFs_mafft_prank" "UGGT2" 1721 12 "0.271849324024" "0.248" "Y" 0.015 15 "154, 156, 623, 677, 691, 738, 780, 876, 915, 932, 1051, 1174, 1301, 1329, 1349" "N" "0.9999994895407719" 0 "na" "N" "0.4009484925650369" 0 "na" "N" "1.0" 0 "na" "N" "0.3686159363035691" 0 "na" "" "" "shared"
+"423" "UPF1" "UPF1_sequences_filtered_longestORFs_mafft_mincov_prank" "UPF1_all" 1740 24 "na" "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "na" "na" 0 "na" "UPF1_sequences_filtered_longestORFs_mafft_prank" "UPF1" 1268 12 "0.005967468791" "0.004" "N" 1 0 "na" "N" "0.9999999999008651" 0 "na" "N" "0.9999900181399214" 0 "na" "N" "0.9940179640545284" 0 "na" "N" "0.9940179640545284" 0 "na" "" "" "shared"
+"424" "USP13" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "USP13_sequences_filtered_longestORFs_mafft_prank" "USP13" 957 12 "0.037174112882" "0.037" "N" 1 2 "374, 873" "N" "0.9999987827948775" 0 "na" "Y" "0.0190013570231371" 2 "586, 706" "N" "1.0" 0 "na" "N" "0.99900049983408" 0 "na" "" "" "onlybats"
+"425" "USP54" "USP54_sequences_filtered_longestORFs_mafft_mincov_prank" "USP54_all" 2486 24 "0.386068465868" "0.385" "N" "0.6967" 22 "464, 1198, 1478, 1525, 1562, 1591, 1627, 1635, 1688, 1712, 1765, 1784, 1862, 1875, 1988, 1989, 1996, 2118, 2234, 2341, 2347, 2410" "Y" "4.585969349940591e-12" 2 "1478, 2234" "Y" "1.025159258712707e-12" 2 "1478, 2234" "Y" "6.791054347170535e-13" 2 "1478, 2234" "na" "na" 0 "na" "USP54_sequences_filtered_longestORFs_mafft_prank" "USP54" 2053 11 "0.366806019369" "0.362" "Y" 0.0301 11 "845, 1129, 1160, 1290, 1291, 1405, 1412, 1732, 1823, 1939, 1985" "N" "0.9997345689145414" 0 "na" "N" "0.15291027386116157" 0 "na" "N" "0.5927396589958697" 0 "na" "N" "0.31192266203294183" 0 "na" "" "" "shared"
+"426" "VPS11" "VPS11_sequences_filtered_longestORFs_mafft_mincov_prank" "VPS11_all" 1500 24 "0.048270606305" "0.042" "N" "0.5166" 5 "440, 528, 682, 787, 854" "N" "0.9999985946152136" 0 "na" "Y" "0.0008361633364003558" 3 "789, 854, 1373" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "VPS11_sequences_filtered_longestORFs_mafft_prank" "VPS11" 1166 12 "0.078603582166" "0.072" "N" 0.0824 5 "27, 304, 314, 591, 596" "N" "0.9999993365374775" 0 "na" "Y" "0.012111394464395" 4 "21, 63, 342, 596" "N" "1.0" 0 "na" "N" "0.5117085777865054" 0 "na" "" "" "shared"
+"427" "VPS39" "VPS39_sequences_filtered_longestORFs_mafft_mincov_prank" "VPS39_all" 1501 23 "0.046946875948" "0.052" "Y" "0.0000" 6 "68, 135, 146, 169, 225, 706" "Y" "7.272055658525019e-16" 1 "146" "Y" "2.5399423605918594e-30" 1 "146" "Y" "2.7057022431548876e-16" 1 "146" "Y" "1.5006105308565566e-22" 1 "146" "VPS39_sequences_filtered_longestORFs_mafft_prank" "VPS39" 1042 12 "0.056596878456" "0.060" "Y" 0 4 "79, 115, 930, 933" "Y" "0.0036263867910577537" 1 "115" "Y" "3.2872363224224216e-11" 3 "115, 464, 723" "Y" "0.002538961855010523" 1 "115" "Y" "1.5934882242290877e-05" 1 "115" "position 115 due to internal splice variant" "" "shared"
+"428" "WASHC4" "WASHC4_sequences_filtered_longestORFs_mafft_mincov_prank" "WASHC4_all" 1602 23 "0.054671143559" "0.054" "Y" "0.0000" 32 "191, 361, 416, 453, 483, 510, 541, 571, 577, 602, 606, 763, 798, 802, 909, 818, 846, 850, 885, 891, 941, 1013, 1027, 1077, 1185, 1211, 1220, 1404, 1432, 1439, 1445, 1447" "N" "0.9934604233737435" 0 "na" "Y" "0.00020410173498656788" 3 "891, 1447, 1448" "N" "0.835270211411029" 0 "na" "N" "0.18787094775098143" 0 "na" "WASHC4_sequences_filtered_longestORFs_mafft_prank" "WASHC4" 1291 12 "0.047673831087" "0.043" "Y" 2e-04 1 "37" "N" "0.9999992783153051" 0 "na" "Y" "9.046577638308179e-07" 16 "37, 242, 245, 389, 506, 578, 630, 1073, 1084, 1152, 1176, 1207, 1208, 1267, 1275, 1278" "N" "0.9990004998331715" 0 "na" "N" "0.5127330190420621" 0 "na" "" "" "shared"
+"429" "WFS1" "WFS1_sequences_filtered_longestORFs_mafft_mincov_prank" "WFS1_all" 1072 24 "0.081575261516" "0.056" "N" "0.2613" 6 "78, 118, 486, 768, 806, 1004" "N" "0.9999996897186547" 0 "na" "Y" "9.570229689317189e-07" 5 "101, 118, 125, 230, 772" "N" "0.39971639333834935" 0 "na" "Y" "2.184769995878869e-06" 2 "118, 230" "WFS1_sequences_filtered_longestORFs_mafft_prank" "WFS1" 1109 11 "0.115587068116" "0.087" "Y" 0.0287 10 "166, 217, 483, 542, 647, 749, 768, 790, 888, 893" "N" "0.9999992486685281" 0 "na" "Y" "0.03804197055110089" 1 "166" "N" "1.0" 0 "na" "N" "0.5449833692075639" 0 "na" "" "" "shared"
+"430" "WFS1[0-2346]" "WFS1_sequences_filtered_longestORFs_mafft_mincov_prank_frag0to2346" "WFS1_all[0-2346]" 782 24 "0.110155273852" "0.078" "N" "0.4926" 5 "69, 118, 374, 486, 768" "N" "0.9999999833444236" 0 "na" "Y" "2.573536088277023e-05" 5 "101, 118, 125, 230, 772" "N" "1.0" 0 "na" "Y" "8.36043582541349e-06" 2 "118, 230" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "onlyprimates"
+"431" "WFS1[2345-3216]" "WFS1_sequences_filtered_longestORFs_mafft_mincov_prank_frag2345to3216" "WFS1_all[2345-3216]" 290 24 "0.021378658292" "0.016" "N" "0.5279" 2 "24, 222" "N" "0.9999999893580026" 0 "na" "N" "0.9312768299514572" 0 "na" "N" "1.0" 0 "na" "N" "0.9990004998331715" 0 "na" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "onlyprimates"
+"432" "YIF1A" "YIF1A_sequences_filtered_longestORFs_mafft_mincov_prank_part1_prank" "YIF1A_all_part1" 1223 24 "0.122099669920" "0.108" "N" "1.0000" 1 "190" "N" "0.9999998503785831" 0 "na" "N" "0.9986341687072853" 0 "na" "N" "0.7276027884144418" 0 "na" "N" "0.2608003778811103" 0 "na" "YIF1A_sequences_filtered_longestORFs_mafft_prank_part2_prank" "YIF1A_part2" 307 12 "0.092980087519" "0.083" "N" 1 0 "na" "N" "0.9999994430788052" 0 "na" "N" "0.9999999928145371" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "dupl yes" "" "shared"
+"433" "YIF1B" "YIF1A_sequences_filtered_longestORFs_mafft_mincov_prank_part2_prank" "YIF1A_all_part2" 682 11 "0.052814080269" "0.068" "N" "0.3729" 0 "na" "N" "0.9999997896859661" 0 "na" "N" "0.7552477206523797" 0 "na" "N" "0.34472785476720136" 0 "na" "N" "0.7641432556483685" 0 "na" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "onlyprimates"
+"434" "ZC3H18" "ZC3H18_sequences_filtered_longestORFs_mafft_mincov_prank" "ZC3H18_all" 1100 24 "0.087671644891" "0.083" "N" "0.6012" 3 "722, 782, 981" "N" "0.9999993848816375" 0 "na" "Y" "0.015299480271226013" 0 "" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "ZC3H18_sequences_filtered_longestORFs_mafft_prank" "ZC3H18" 1226 11 "0.200106682861" "0.187" "Y" 0.0016 4 "54, 654, 771, 1080" "N" "0.9999991996195169" 0 "na" "N" "0.5258352764131282" 0 "na" "N" "1.0" 0 "na" "N" "0.05596661089965757" 0 "na" "" "" "shared"
+"435" "ZC3H18[0-1101]" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "ZC3H18_sequences_filtered_longestORFs_mafft_prank_frag0to1101" "ZC3H18[0-1101]" 367 11 "0.229802082341" "0.219" "Y" 0.0191 3 "54, 148, 163" "N" "0.9999990616263259" 0 "na" "N" "0.24086994381226873" 0 "na" "Y" "0.0005745060096894928" 1 "188" "Y" "0.00030751090743914297" 1 "188" "" "" "onlybats"
+"436" "ZC3H18[1100-3678]" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "ZC3H18_sequences_filtered_longestORFs_mafft_prank_frag1100to3678" "ZC3H18[1100-3678]" 859 11 "0.204731954234" "0.189" "N" 0.7392 4 "287, 404, 713, 744" "N" "0.9999982891136908" 0 "na" "N" "0.781377329393951" 0 "na" "N" "1.0" 0 "na" "N" "0.46301306831102595" 0 "na" "" "" "onlybats"
+"437" "ZC3H7A" "ZC3H7A_sequences_filtered_longestORFs_mafft_mincov_prank" "ZC3H7A_all" 1242 24 "0.100883053669" "0.091" "Y" "0.0003" 8 "35, 150, 272, 389, 423, 540, 614, 1033" "N" "0.9999988073966796" 0 "na" "N" "0.9433840075471273" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "ZC3H7A_sequences_filtered_longestORFs_mafft_prank" "ZC3H7A" 1018 12 "0.207349246144" "0.173" "N" 0.9537 6 "194, 313, 318, 464, 606, 884" "N" "0.9999992934629285" 0 "na" "Y" "0.04687509899081552" 6 "92, 183, 216, 299, 318, 464" "N" "0.9314618921276734" 0 "na" "N" "0.3305491224578773" 0 "na" "" "" "shared"
+"438" "ZDHHC5" "ZDHHC5_sequences_filtered_longestORFs_mafft_mincov_prank" "ZDHHC5_all" 823 24 "0.078488206473" "0.075" "Y" "0.0351" 2 "597, 742" "N" "0.9848981471344455" 0 "na" "Y" "0.013502502486699652" 2 "404, 597" "N" "1.0" 0 "na" "N" "0.49213608756256844" 0 "na" "ZDHHC5_sequences_filtered_longestORFs_mafft_prank" "ZDHHC5" 768 12 "0.080123114130" "0.080" "N" 1 1 "95" "N" "0.8751057533143412" 0 "na" "Y" "0.00028950851490339055" 3 "95, 387, 688" "N" "1.0" 0 "na" "N" "0.26820598310847715" 0 "na" "" "" "shared"
+"439" "ZNF318" "ZNF318_sequences_filtered_longestORFs_mafft_mincov_prank" "ZNF318_all" 2496 24 "0.335852925463" "0.343" "Y" "0.0000" 32 "38, 75, 78, 104, 174, 392, 443, 703, 799, 1177, 1372, 1492, 1636, 1646, 1647, 1663, 1814, 1897, 1929, 1946, 1995, 2088, 2098, 2166, 2181, 2243, 2249, 2250, 2287, 2356, 2372, 2483" "Y" "0.0010039629225922107" 0 "" "Y" "1.3246467997073662e-05" 2 "1636, 2098" "Y" "7.829709942783089e-05" 2 "1636, 2098" "Y" "1.1348614329410036e-06" 6 "1636, 1817, 1929, 1954, 2098, 2243" "ZNF318_sequences_filtered_longestORFs_mafft_prank" "ZNF318" 2395 11 "0.361499795329" "0.353" "N" 0.1184 0 "na" "N" "0.8750270725798085" 0 "na" "N" "0.5452621832627409" 0 "na" "N" "0.6505090947231271" 0 "na" "N" "0.11567161588366141" 0 "na" "" "" "shared"
+"440" "ZNF503" "ZNF503_sequences_filtered_longestORFs_mafft_mincov_prank" "ZNF503_all" 802 21 "0.049882463869" "0.026" "N" "1.0000" 1 "87" "N" "0.9999980745506383" 0 "na" "Y" "0.024559140884415645" 1 "177" "N" "1.0" 0 "na" "N" "0.6206425292935231" 0 "na" "ZNF503_sequences_filtered_longestORFs_mafft_prank" "ZNF503" 682 9 "0.036470300914" "0.033" "N" 1 0 "na" "N" "0.9999987418249204" 0 "na" "N" "0.7780311233967817" 0 "na" "N" "1.0" 0 "na" "N" "1.0" 0 "na" "" "" "shared"
+"441" "ZYG11B" "ZYG11B_sequences_filtered_longestORFs_mafft_mincov_prank" "ZYG11B_all" 1128 24 "0.023655415579" "0.025" "Y" "0.0000" 1 "998" "N" "0.9999975270769591" 0 "na" "Y" "0.020268109682591493" 4 "896, 990, 993, 998" "N" "1.0" 0 "na" "N" "0.6757041139607441" 0 "na" "ZYG11B_sequences_filtered_longestORFs_mafft_prank" "ZYG11B" 854 12 "0.019630434764" "0.021" "N" 1 0 "na" "N" "0.9999984077343413" 0 "na" "N" "0.1157682212961436" 0 "na" "N" "1.0" 0 "na" "N" "0.6750287475861135" 0 "na" "" "" "shared"
+"442" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "TMPRSS2_bat_select_cut_mafft_prank" "TMPRSS2" 574 12 "0.129489038364869" "0.127" "N" 0.9358 19 "59, 73, 78, 108, 115, 117, 121, 133, 144, 241, 259, 288, 321, 403, 421, 451, 455, 466, 573" "N" "0.999999906049202" 0 "na" "N" "0.334893426994811" 0 "na" "N" "1.0" 0 "na" "N" "0.4210515526274131" 0 "na" "" "" "onlybats"
diff --git a/covid_comp_script0_table.pdf b/covid_comp_script0_table.pdf
index 9676ae3a3d1aa7285328509717f93debf83197cb..61c6b0cd912e496baabfe8af0ce44a00c767dcfc 100644
Binary files a/covid_comp_script0_table.pdf and b/covid_comp_script0_table.pdf differ
diff --git a/covid_comp_script0_table.tex b/covid_comp_script0_table.tex
index a591a5a6ab05a19bc7a4f2cd1ea6b30b10daa0f9..4186e733d21a48d00b71018b7288317aafa90698 100644
--- a/covid_comp_script0_table.tex
+++ b/covid_comp_script0_table.tex
@@ -1066,9 +1066,11 @@ TMPRSS2 in bats
\begin{alltt}
\hlcom{# keeping the uncut one}
\hlcom{# renaming the other one TMPRSS2_cut}
-\hlstd{dginnbats[dginnbats}\hlopt{$}\hlstd{bats.File}\hlopt{==}\hlstr{"TMPRSS2_bat_select_cut_mafft_prank"}\hlstd{,}\hlstr{"Gene.name"}\hlstd{]}\hlkwb{<-}\hlstr{"TMPRSS2_cut"}
+\hlstd{dginnbats[dginnbats}\hlopt{$}\hlstd{bats_File}\hlopt{==}\hlstr{"TMPRSS2_bat_select_cut_mafft_prank"}\hlstd{,}\hlstr{"Gene.name"}\hlstd{]}\hlkwb{<-}\hlstr{"TMPRSS2_cut"}
\end{alltt}
-\end{kframe}
+
+
+{\ttfamily\noindent\color{warningcolor}{\#\# Warning in `[<-.factor`(`*tmp*`, iseq, value = "{}TMPRSS2\_cut"{}): invalid factor level, NA generated}}\end{kframe}
\end{knitrout}
RIPK1: ANcestral version kept, suppress it "RIPK1\_sequences\_filtered\_longestORFs\_mafft\_mincov\_prank"
@@ -1119,7 +1121,8 @@ GNG5
\end{verbatim}
\begin{alltt}
\hlcom{# genes in common}
-\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name]}
+\hlstd{common}\hlkwb{<-}\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name]}
+\hlstd{common}
\end{alltt}
\begin{verbatim}
## [1] "AAR2" "AASS" "AATF" "ABCC1" "ACAD9"
@@ -1196,7 +1199,8 @@ GNG5
\end{verbatim}
\begin{alltt}
\hlcom{# genes only in primates}
-\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[(dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\hlstd{onlyprimates}\hlkwb{<-}\hlstd{dginnT}\hlopt{$}\hlstd{Gene.name[(dginnT}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\hlstd{onlyprimates}
\end{alltt}
\begin{verbatim}
## [1] "ADAM9[0-3120]" "ADAM9[3119-3927]" "ATP5MGL"
@@ -1238,7 +1242,8 @@ GNG5
\end{verbatim}
\begin{alltt}
\hlcom{# genes only in bats}
-\hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name[(dginnbats}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\hlstd{onlybats}\hlkwb{<-}\hlstd{dginnbats}\hlopt{$}\hlstd{Gene.name[(dginnbats}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{]}
+\hlstd{onlybats}
\end{alltt}
\begin{verbatim}
## [1] "ADAM9[0-2769]" "ADAM9[2768-3030]" "ARL6IP6"
@@ -1250,16 +1255,45 @@ GNG5
## [19] "SIGMAR1" "SLC44A2[0-2820]" "SLC44A2[2819-3792]"
## [22] "TLE5" "USP13" "ZC3H18[0-1101]"
## [25] "ZC3H18[1100-3678]" "FGFR1OP" "ELOB"
-## [28] "REEP6_like" "SELENOS"
+## [28] "REEP6_like" "SELENOS" NA
\end{verbatim}
\begin{alltt}
\hlkwd{length}\hlstd{(dginnbats}\hlopt{$}\hlstd{Gene.name[(dginnbats}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlnum{FALSE}\hlstd{])}
\end{alltt}
\begin{verbatim}
-## [1] 29
+## [1] 30
\end{verbatim}
\end{kframe}
\end{knitrout}
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(dginnT, dginnbats,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{,} \hlkwc{all.x}\hlstd{=T,} \hlkwc{all.y}\hlstd{=T)}
+\hlkwd{dim}\hlstd{(tab)}
+\end{alltt}
+\begin{verbatim}
+## [1] 442 55
+\end{verbatim}
+\begin{alltt}
+\hlcom{# add column "shared"/"only bats"/"only primates"}
+\hlstd{tab}\hlopt{$}\hlstd{status}\hlkwb{<-}\hlstr{""}
+\hlstd{tab}\hlopt{$}\hlstd{status[tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{common]}\hlkwb{<-}\hlstr{"shared"}
+\hlstd{tab}\hlopt{$}\hlstd{status[tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{onlyprimates]}\hlkwb{<-}\hlstr{"onlyprimates"}
+\hlstd{tab}\hlopt{$}\hlstd{status[tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{onlybats]}\hlkwb{<-}\hlstr{"onlybats"}
+\hlkwd{table}\hlstd{(tab}\hlopt{$}\hlstd{status)}
+\end{alltt}
+\begin{verbatim}
+##
+## onlybats onlyprimates shared
+## 30 89 323
+\end{verbatim}
+\begin{alltt}
+\hlkwd{write.table}\hlstd{(tab,} \hlstr{"covid_comp_alldginn.txt"}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
\end{document}