printCNOGpro: Prints the results of a 'CNOGpro' experiment
In CNOGpro: Copy Numbers of Genes in prokaryotes
Description
Usage
Arguments
Author(s)
See Also
Examples
Description
Results are printed to stout. The default behavior is to print
the HMMtable. If this does not exist, the function will attempt
to print the gene table (with copy numbers.)
Usage
1
printCNOGpro(experiment)
Arguments
experiment
An object of class CNOGpro
Author(s)
Ola Brynildsrud
See Also
Examples
1
2
3
4
data(carsonella)
carsonella_normalized <- normalizeGC(carsonella)
carsonella_bootstrapped <- runBootstrap(carsonella_normalized, quantiles=c(0.01,0.99))
printCNOGpro(carsonella_bootstrapped)
Example output
Loading required package: seqinr
Normalizing read counts for GC bias...
Overall values for chromosome CP003467 :
Median read count: 66
Median GC percentage: 0.17
Calculating per-read weight based on GC percentage...
Successfully normalized chromosome CP003467
Starting bootstrap analysis for CP003467 - This might take a while...
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Finished bootstrap analysis.
CNOGpro results for C. Carsonella ruddii, artificial example data. Chromosome: CP003467
Type Locus Strand Left Right Length CN_boot Lowerbound
1 CDS CRDC_00005 1 1 1332 1332 0.9692635 0.86784307
2 CDS CRDC_00010 1 1332 2840 1509 1.0283747 0.95924658
3 CDS CRDC_00015 1 2806 3498 693 0.9778032 0.87314839
4 IG 1 3499 3499 1 0.7771187 0.01494459
5 CDS CRDC_00020 1 3500 3730 231 0.9116200 0.81074405
6 IG 1 3731 3735 5 1.0461214 0.01494459
7 CDS CRDC_00030 1 3736 4191 456 0.9564538 0.83091925
8 CDS CRDC_00035 1 4184 4366 183 1.0909551 1.06106595
9 IG 1 4367 4367 1 1.1058997 0.01494459
10 CDS CRDC_00040 1 4368 5813 1446 0.9508496 0.84623746
11 CDS CRDC_00045 1 5810 6562 753 0.9284327 0.84250131
12 CDS CRDC_00050 1 6559 7902 1344 0.9365277 0.87077149
13 CDS CRDC_00055 1 7899 8141 243 1.0797467 0.95645381
14 CDS CRDC_00060 1 8128 9015 888 0.9310480 0.84287492
15 IG 1 9016 9259 244 1.0760105 0.94150922
16 CDS CRDC_00070 -1 9260 9703 444 0.9713984 0.87425856
17 CDS CRDC_00075 -1 9679 11586 1908 0.8944338 0.83762937
18 CDS CRDC_00080 1 11564 13222 1659 0.9730589 0.89666715
19 CDS CRDC_00085 1 13203 13922 720 1.0386491 0.98447492
20 CDS CRDC_00090 -1 13910 14062 153 1.1058997 0.94150922
21 IG 1 14063 14190 128 1.2404010 1.21051186
22 tRNA CRDC_t01077 1 14191 14264 74 1.0087599 0.80700791
23 CDS CRDC_00095 -1 14252 15301 1050 1.0087599 0.91909234
24 CDS CRDC_00100 -1 15301 16245 945 0.9370258 0.84734336
25 CDS CRDC_00105 -1 16242 16943 702 0.9975514 0.92096041
26 CDS CRDC_00110 1 16923 17576 654 0.9756683 0.90094533
27 CDS CRDC_00115 1 17570 18196 627 0.9479140 0.83262720
28 CDS CRDC_00120 1 18171 18716 546 1.1955673 0.96072370
29 CDS CRDC_00125 1 18709 22044 3336 2.0368598 1.90938246
30 CDS CRDC_00130 1 22041 22526 486 0.9464908 0.85928907
31 IG 1 22527 22562 36 0.8368971 0.01494459
32 CDS CRDC_00135 1 22563 24635 2073 0.9122993 0.85250739
33 CDS CRDC_00140 -1 24632 24949 318 0.9938153 0.88546701
34 CDS CRDC_00145 1 24948 25139 192 0.8867124 0.82195250
35 CDS CRDC_00150 1 25114 25554 441 0.7502185 0.59467516
36 CDS CRDC_00155 1 25551 26567 1017 0.9333576 0.83553849
37 CDS CRDC_00160 1 26557 28203 1647 1.0411398 0.96474806
38 CDS CRDC_00165 1 28196 29179 984 1.0366112 0.94694362
39 IG 1 29180 29186 7 1.2553456 0.02988918
40 CDS CRDC_00170 1 29187 30392 1206 1.1047501 1.03002718
41 CDS CRDC_00175 -1 30379 30939 561 0.9543189 0.91588992
42 CDS CRDC_00180 1 30932 31075 144 0.8966755 0.82195250
43 CDS CRDC_00185 1 31072 32277 1206 0.8736838 0.77480806
44 CDS CRDC_00190 1 32274 33623 1350 0.9793689 0.90265329
45 CDS CRDC_00195 1 33620 34285 666 0.9735333 0.84757180
46 CDS CRDC_00200 1 34276 35097 822 1.0594054 0.88837290
47 IG 1 35098 35099 2 0.6725066 0.01494459
48 CDS CRDC_00205 1 35100 36245 1146 1.0173818 0.93115147
49 CDS CRDC_00210 -1 36207 37085 879 0.9581143 0.89333783
50 IG 1 37086 37086 1 0.9713984 0.01494459
51 CDS CRDC_00215 -1 37087 37302 216 1.0050237 0.91535619
52 IG 1 37303 37319 17 1.1656781 0.01494459
53 tRNA CRDC_t01079 1 37320 37390 71 1.1656781 0.01494459
54 tRNA CRDC_t01081 1 37391 37462 72 1.0760105 0.98634300
55 tRNA CRDC_t01083 1 37463 37551 89 1.1283166 0.98634300
56 CDS CRDC_00220 -1 37543 37839 297 1.0274406 0.90041160
57 CDS CRDC_00225 -1 37836 39131 1296 1.0578635 0.98951338
58 CDS CRDC_00230 1 39120 40364 1245 0.9794455 0.86908544
59 CDS CRDC_00235 1 40361 40882 522 1.0610660 0.94150922
60 CDS CRDC_00240 1 40879 41745 867 0.9803652 0.88322532
61 CDS CRDC_00245 1 41742 42482 741 0.9303008 0.78083619
62 IG 1 42483 42484 2 0.7322850 0.01494459
63 tRNA CRDC_t01085 1 42485 42557 73 0.8443694 0.73228495
64 tRNA CRDC_t01087 -1 42558 42630 73 1.0237045 0.95645381
65 IG 1 42631 42659 29 1.0909551 0.02988918
66 CDS CRDC_00255 -1 42660 43106 447 1.1308074 0.99379038
67 CDS CRDC_00260 -1 43096 44019 924 0.9387920 0.83960070
68 CDS CRDC_00265 1 44020 44712 693 1.0031557 0.92467788
69 CDS CRDC_00270 -1 44702 45778 1077 0.9496608 0.87086207
70 CDS CRDC_00275 -1 45765 47120 1356 0.9365277 0.86479366
71 CDS CRDC_00280 -1 47104 47301 198 1.0710290 1.03117677
72 CDS CRDC_00285 1 47291 47836 546 1.0653358 1.02050206
73 CDS CRDC_00290 1 47817 49058 1242 1.0231297 0.95415465
74 CDS CRDC_00295 1 49055 49351 297 1.0573298 0.93777308
75 CDS CRDC_00300 1 49348 49728 381 0.9833541 0.91756799
76 IG 1 49729 49872 144 0.9116200 0.89667545
77 CDS CRDC_00305 1 49873 50445 573 1.0888202 0.98207311
78 CDS CRDC_00310 1 50426 51178 753 0.9732665 0.88918447
79 CDS CRDC_00315 1 51175 52401 1227 0.9585888 0.89131675
80 CDS CRDC_00320 1 52388 53512 1125 0.9955397 0.94725714
81 CDS CRDC_00325 -1 53509 55101 1593 0.9388719 0.87116416
82 IG 1 55102 55107 6 1.0909551 0.01494459
83 CDS CRDC_00330 -1 55108 55392 285 1.0261952 0.95645381
84 IG 1 55393 55523 131 1.1058997 1.03117677
85 tRNA CRDC_t01089 1 55524 55596 73 1.2105119 0.01494459
86 IG 1 55597 55601 5 1.0535937 0.89667545
87 tRNA CRDC_t01091 1 55602 55675 74 0.8966755 0.01494459
88 IG 1 55676 55798 123 0.7696464 0.64261741
89 CDS CRDC_00340 1 55799 56260 462 0.8966755 0.74722954
90 CDS CRDC_00345 1 56260 56724 465 0.9514723 0.84431957
91 CDS CRDC_00350 1 56717 57868 1152 1.0286860 0.92904294
92 CDS CRDC_00355 1 57840 58379 540 1.0187229 0.94898152
93 CDS CRDC_00360 1 58357 58485 129 0.9415092 0.91162004
94 CDS CRDC_00365 1 58482 59249 768 0.8916939 0.81863148
95 CDS CRDC_00370 1 59246 60316 1071 0.9701530 0.87673688
96 IG 1 60317 60320 4 0.8817309 0.01494459
97 tRNA CRDC_t01093 1 60321 60392 72 0.8817309 0.01494459
98 CDS CRDC_00375 -1 60384 61319 936 1.0080806 0.90206909
99 CDS CRDC_00380 -1 61316 62047 732 1.0573298 0.97513455
100 CDS CRDC_00385 -1 62044 62721 678 1.0442533 0.97326648
101 CDS CRDC_00390 -1 62718 63320 603 0.8838658 0.77925367
102 CDS CRDC_00395 -1 63317 63859 543 1.0012876 0.90907946
103 IG 1 63860 63866 7 0.9415092 0.01494459
104 tRNA CRDC_t01095 1 63867 63939 73 0.9340369 0.92656463
105 tRNA CRDC_t01097 1 63940 64010 71 0.9863430 0.92656463
106 IG 1 64011 64012 2 1.0461214 0.01494459
107 tRNA CRDC_t01099 1 64013 64084 72 1.0461214 0.01494459
108 IG 1 64085 64250 166 0.8667863 0.64261741
109 CDS CRDC_00400 -1 64251 64583 333 0.8406332 0.67624274
110 CDS CRDC_00405 1 64584 65036 453 0.9166016 0.82942479
111 IG 1 65037 65097 61 0.7920633 0.01494459
112 CDS CRDC_00415 1 65098 66903 1806 0.9557066 0.88919568
113 IG 1 66904 66953 50 0.9265646 0.01494459
114 CDS CRDC_00420 1 66954 67652 699 0.9377731 0.87610796
115 CDS CRDC_00425 1 67646 68098 453 0.8279303 0.76217413
116 CDS CRDC_00430 1 68091 68642 552 0.9671285 0.86249504
117 CDS CRDC_00435 1 68632 71529 2898 1.0341657 0.97836258
118 IG 1 71530 71533 4 0.8966755 0.01494459
119 tRNA CRDC_t01101 1 71534 71614 81 0.9265646 0.89667545
120 IG 1 71615 71622 8 0.9564538 0.01494459
121 CDS CRDC_00440 1 71623 73176 1554 1.0620000 0.97326648
122 CDS CRDC_00445 1 73163 73357 195 0.8468601 0.71734036
123 CDS CRDC_00450 1 73354 74283 930 1.0042765 0.95344995
124 CDS CRDC_00455 1 74276 75442 1167 0.9645009 0.89552587
125 IG 1 75443 75448 6 0.9863430 0.01494459
126 tRNA CRDC_t01103 1 75449 75522 74 0.9265646 0.86678627
127 tRNA CRDC_t01105 1 75523 75595 73 0.8667863 0.01494459
128 IG 1 75596 75597 2 0.8667863 0.01494459
129 tRNA CRDC_t01107 1 75598 75673 76 0.9489815 0.86678627
130 IG 1 75674 75693 20 1.0311768 0.01494459
131 CDS CRDC_00460 1 75694 76272 579 0.9820731 0.87532604
132 CDS CRDC_00465 1 76253 77326 1074 0.9788707 0.91286542
133 CDS CRDC_00470 1 77326 78420 1095 0.9664169 0.86927703
134 CDS CRDC_00475 1 78417 79682 1266 0.9472571 0.88171936
135 CDS CRDC_00480 1 79669 79878 210 0.8568232 0.71734036
136 IG 1 79879 79924 46 1.0610660 1.00128759
137 tRNA CRDC_t01109 1 79925 80009 85 0.9938153 0.86678627
138 IG 1 80010 80074 65 0.8667863 0.01494459
139 CDS CRDC_00485 1 80075 80572 498 1.0560844 0.85679830
140 CDS CRDC_00490 -1 80573 83617 3045 1.0110950 0.95131661
141 IG 1 83618 83625 8 1.0610660 0.01494459
142 CDS CRDC_00495 1 83626 84984 1359 1.0503912 0.94791405
143 CDS CRDC_00500 1 84977 86014 1038 0.8792401 0.80824083
144 CDS CRDC_00505 1 86007 87371 1365 0.9767358 0.90520454
145 CDS CRDC_00510 1 87355 87909 555 1.0140972 0.88170951
146 CDS CRDC_00515 1 87902 88948 1047 0.9469436 0.82601471
147 CDS CRDC_00520 1 88941 89969 1029 1.0393284 0.90615847
148 CDS CRDC_00525 1 89966 90523 558 0.9692635 0.83894663
149 IG 1 90524 90526 3 0.7322850 0.01494459
150 CDS CRDC_00530 1 90527 91540 1014 0.9944946 0.89528968
151 tRNA CRDC_t01111 1 91520 91598 79 0.8368971 0.01494459
152 IG 1 91599 91608 10 0.9564538 0.83689709
153 CDS CRDC_00535 1 91609 92349 741 0.9396411 0.86303144
154 CDS CRDC_00540 1 92339 92710 372 0.9086311 0.83091925
155 CDS CRDC_00545 -1 92698 93027 330 0.9863430 0.94449814
156 CDS CRDC_00550 -1 93020 93562 543 0.9664169 0.86678627
157 CDS CRDC_00555 -1 93549 94112 564 0.9116200 0.59351375
158 CDS CRDC_00560 -1 94109 95335 1227 0.1253046 0.00000000
159 IG 1 95336 95409 74 1.2404010 1.21051186
160 CDS CRDC_00565 1 95410 95619 210 1.1507335 1.06106595
161 IG 1 95620 95989 370 1.0050237 0.82942479
162 CDS CRDC_00570 -1 95990 96304 315 0.9355314 0.78309656
163 CDS CRDC_00575 -1 96288 96482 195 0.9166016 0.71734036
164 CDS CRDC_00580 -1 96430 96960 531 0.9215831 0.80200147
165 CDS CRDC_00585 -1 96960 97568 609 0.9692635 0.86249504
166 IG 1 97569 97602 34 0.9639261 0.85184168
167 CDS CRDC_00590 -1 97603 98067 465 1.0371546 0.90265329
168 CDS CRDC_00595 -1 98048 99706 1659 0.9938153 0.93652769
169 CDS CRDC_00600 -1 99690 100616 927 1.0434042 0.93743343
170 CDS CRDC_00605 -1 100604 100729 126 0.9863430 0.92656463
171 CDS CRDC_00610 1 100728 101990 1263 1.0346255 0.98287125
172 CDS CRDC_00615 1 101980 102255 276 1.1208443 1.03864906
173 CDS CRDC_00620 1 102242 103780 1539 0.9956834 0.94524537
174 IG 1 103781 103901 121 0.9763799 0.92656463
175 CDS CRDC_00630 1 103902 104132 231 1.0212137 0.92656463
176 CDS CRDC_00635 -1 104116 104940 825 1.0527634 0.94813466
177 CDS CRDC_00640 -1 104933 105976 1044 0.9781914 0.86677268
178 CDS CRDC_00645 -1 105963 106940 978 0.9605296 0.91568225
179 IG 1 106941 106942 2 1.0461214 0.01494459
180 tRNA CRDC_t01113 -1 106943 107015 73 1.0237045 1.00128759
181 IG 1 107016 107107 92 0.9489815 0.89667545
182 CDS CRDC_00650 1 107108 108400 1293 0.9208167 0.84950802
183 CDS CRDC_00655 1 108390 108575 186 1.0311768 0.89667545
184 CDS CRDC_00660 -1 108568 109743 1176 0.9518555 0.88976645
185 IG 1 109744 109778 35 0.9713984 0.01494459
186 tRNA CRDC_t01115 1 109779 109849 71 0.9788707 0.97139841
187 IG 1 109850 109852 3 0.9863430 0.01494459
188 tRNA CRDC_t01117 1 109853 109933 81 0.9863430 0.98634300
189 CDS CRDC_00665 -1 109915 110691 777 1.0442533 0.95639777
190 IG 1 110692 110709 18 1.0012876 0.89667545
191 tRNA CRDC_t01119 -1 110710 110783 74 0.8966755 0.01494459
192 CDS CRDC_00670 -1 110761 111081 321 1.0311768 0.86305012
193 CDS CRDC_00675 1 111075 112472 1398 0.9664169 0.87674933
194 tRNA CRDC_t01121 -1 112438 112510 73 1.1357889 1.10589972
195 IG 1 112511 112515 5 1.1656781 0.01494459
196 tRNA CRDC_t01123 -1 112516 112597 82 1.1656781 0.01494459
197 CDS CRDC_00680 -1 112575 113822 1248 1.0098274 0.91695740
198 CDS CRDC_00685 -1 113819 114811 993 1.0216666 0.92520603
199 CDS CRDC_00690 -1 114804 115706 903 1.0027820 0.88621424
200 CDS CRDC_00695 1 115671 117545 1875 0.9317952 0.84359974
201 CDS CRDC_00700 1 117517 118044 528 1.1258258 1.00377835
202 CDS CRDC_00705 -1 118037 118936 900 0.9639261 0.83689709
203 CDS CRDC_00710 -1 118933 119664 732 1.0199683 0.92469656
204 CDS CRDC_00715 -1 119661 120800 1140 1.0361583 0.91907988
205 IG 1 120801 120807 7 0.8667863 0.01494459
206 rRNA CRDC_r01133 -1 120808 120915 108 0.9116200 0.86678627
207 IG 1 120916 120936 21 0.9564538 0.01494459
208 rRNA CRDC_r01135 -1 120937 123723 2787 1.0177782 0.96676043
209 IG 1 123724 123770 47 1.0760105 0.02988918
210 rRNA CRDC_r01137 -1 123771 125293 1523 1.0031557 0.92935740
211 IG 1 125294 125369 76 1.0087599 0.98634300
212 CDS CRDC_00720 -1 125370 126251 882 1.0461214 0.94298874
213 CDS CRDC_00725 -1 126248 126394 147 0.9415092 0.85184168
214 CDS CRDC_00730 -1 126382 126570 189 0.9963061 0.89667545
215 IG 1 126571 126576 6 0.8966755 0.01494459
216 CDS CRDC_00735 -1 126577 126924 348 1.0042765 0.92354583
217 CDS CRDC_00740 -1 126921 128063 1143 0.9776253 0.89165656
218 CDS CRDC_00745 -1 128060 128869 810 1.0876341 1.01455506
219 CDS CRDC_00750 -1 128862 130169 1308 0.9286996 0.85502274
220 CDS CRDC_00755 -1 130169 131296 1128 1.1656781 1.06852579
221 CDS CRDC_00760 -1 131293 131487 195 1.0511029 0.95645381
222 CDS CRDC_00765 -1 131474 131671 198 0.8916939 0.70239577
223 CDS CRDC_00770 -1 131668 131895 228 1.0112506 0.92656463
224 IG 1 131896 131945 50 1.1058997 1.09095513
225 tRNA CRDC_t01125 1 131946 132018 73 1.0461214 0.97139841
226 IG 1 132019 132022 4 0.9713984 0.02973974
227 CDS CRDC_00775 -1 132023 133018 996 1.0529144 0.99176381
228 CDS CRDC_00780 -1 133019 133471 453 0.9624317 0.78590614
229 CDS CRDC_00785 -1 133392 135068 1677 0.9307159 0.85016456
230 CDS CRDC_00790 -1 135065 135670 606 0.9884779 0.85179898
231 CDS CRDC_00795 -1 135663 135800 138 0.8817309 0.70239577
232 CDS CRDC_00800 -1 135793 135930 138 0.8070079 0.70239577
233 CDS CRDC_00805 -1 135923 138373 2451 1.0090588 0.92058082
234 CDS CRDC_00810 -1 138370 138522 153 1.0511029 0.92656463
235 CDS CRDC_00815 -1 138507 139283 777 1.0237045 0.92467788
236 CDS CRDC_00820 -1 139270 139527 258 0.8630501 0.67250659
237 IG 1 139528 139531 4 0.8518417 0.01494459
238 CDS CRDC_00825 -1 139532 139831 300 0.8256886 0.74722954
239 IG 1 139832 139839 8 0.7920633 0.01494459
240 CDS CRDC_00830 -1 139840 140085 246 0.9016570 0.79206331
241 CDS CRDC_00835 -1 140069 141031 963 0.8980341 0.82466969
242 CDS CRDC_00840 -1 141028 141609 582 0.9948828 0.89667545
243 CDS CRDC_00845 -1 141609 141968 360 0.9900791 0.85931397
244 CDS CRDC_00850 -1 141955 142311 357 0.8608084 0.72923626
245 CDS CRDC_00855 -1 142308 142421 114 0.8667863 0.80700791
246 CDS CRDC_00860 -1 142399 142656 258 0.8929393 0.80700791
247 CDS CRDC_00865 -1 142657 143073 417 1.0939441 1.03416569
248 CDS CRDC_00870 -1 143055 143291 237 1.0859736 1.03117677
249 CDS CRDC_00875 -1 143288 143791 504 0.9913245 0.87425856
250 CDS CRDC_00880 -1 143788 144153 366 1.0999219 0.98030538
251 IG 1 144154 144155 2 0.9265646 0.01494459
252 CDS CRDC_00885 -1 144156 144446 291 1.0610660 0.93403693
253 IG 1 144447 144448 2 1.2852348 0.02988918
254 CDS CRDC_00890 -1 144449 144943 495 1.1258258 0.98634300
255 CDS CRDC_00895 -1 144940 145308 369 0.9444981 0.80700791
256 CDS CRDC_00900 -1 145305 145547 243 0.8717678 0.77711872
257 CDS CRDC_00905 -1 145540 145947 408 1.0102543 0.89966437
258 IG 1 145948 145951 4 1.2404010 0.01494459
259 CDS CRDC_00910 -1 145952 146554 603 0.9906129 0.87746098
260 CDS CRDC_00915 -1 146539 146856 318 0.8406332 0.79206331
261 CDS CRDC_00920 -1 146846 147109 264 1.0124960 0.84436938
262 CDS CRDC_00925 -1 147106 147807 702 1.0816148 0.99751408
263 CDS CRDC_00930 -1 147804 148319 516 1.1706596 1.07100410
264 CDS CRDC_00935 -1 148316 148726 411 1.0192211 0.98036516
265 CDS CRDC_00940 -1 148723 149019 297 1.0124960 0.91909234
266 CDS CRDC_00945 -1 149016 150206 1191 1.0116338 0.91734497
267 IG 1 150207 150225 19 1.2254564 0.02988918
268 CDS CRDC_00950 -1 150226 152262 2037 1.0183671 0.95145805
269 CDS CRDC_00955 -1 152259 152729 471 0.8667863 0.79953561
270 CDS CRDC_00960 -1 152722 153087 366 0.9452454 0.90414775
271 IG 1 153088 153096 9 1.0162322 0.02988918
272 CDS CRDC_00965 -1 153097 156993 3897 0.9934417 0.93365210
273 CDS CRDC_00970 -1 156969 160769 3801 1.0265784 0.97675547
274 CDS CRDC_00975 -1 160766 161110 345 0.9893319 0.89664556
275 CDS CRDC_00980 -1 161091 161525 435 0.9863430 0.88422163
276 CDS CRDC_00985 -1 161522 162094 573 1.0311768 0.85184168
277 CDS CRDC_00990 -1 162087 162500 414 0.9564538 0.76815197
278 IG 1 162501 162519 19 0.8219525 0.01494459
279 tRNA CRDC_t01127 -1 162520 162590 71 0.8219525 0.02973974
280 IG 1 162591 162602 12 0.8817309 0.82195250
281 tRNA CRDC_t01129 -1 162603 162673 71 0.9415092 0.02973974
282 IG 1 162674 162674 1 0.9415092 0.01494459
283 tRNA CRDC_t01131 -1 162675 162755 81 0.8368971 0.73228495
284 IG 1 162756 162812 57 0.7920633 0.73228495
285 CDS CRDC_00995 -1 162813 163088 276 0.9116200 0.83689709
286 CDS CRDC_01000 -1 163055 163558 504 0.8418786 0.81448020
287 CDS CRDC_01005 -1 163551 165356 1806 0.9737581 0.90688497
288 CDS CRDC_01010 -1 165349 166113 765 0.9664169 0.88173086
289 CDS CRDC_01015 1 166090 166839 750 0.8983360 0.75053396
290 CDS CRDC_01020 1 166826 167755 930 0.8623029 0.71282709
291 CDS CRDC_01025 1 167743 167955 213 0.9614353 0.85184168
292 CDS CRDC_01030 1 167946 168410 465 1.0560844 0.94399999
293 CDS CRDC_01035 1 168403 169779 1377 1.0034225 0.91267684
294 CDS CRDC_01040 1 169776 170969 1194 0.9851934 0.93572682
295 CDS CRDC_01045 1 170962 171711 750 0.9016570 0.83854099
296 CDS CRDC_01050 1 171708 172331 624 1.0205021 0.92229475
297 IG 1 172332 172439 108 0.9340369 0.82195250
298 CDS CRDC_01060 1 172440 172988 549 1.0809921 1.02121371
299 IG 1 172989 173016 28 1.0685382 0.94150922
300 CDS CRDC_01065 -1 173017 173220 204 1.0012876 0.94150922
301 IG 1 173221 173286 66 1.0461214 0.01494459
302 CDS CRDC_01070 -1 173287 173964 678 0.9545857 0.75281508
303 IG 1 173965 174014 50 0.8294248 0.67250659
Upperbound
1 1.0589524
2 1.0975027
3 1.0781455
4 0.7771187
5 1.0124960
6 1.0461214
7 1.0610660
8 1.1058997
9 1.1058997
10 1.0582638
11 1.0162322
12 1.0102543
13 1.1619419
14 1.0072654
15 1.2553456
16 1.0635567
17 0.9564688
18 1.0386491
19 1.1002955
20 1.2702902
21 1.2702902
22 1.2105119
23 1.0959616
24 1.0356601
25 1.0834828
26 1.0866852
27 1.0567961
28 1.5115386
29 2.1300569
30 1.0660475
31 0.8368971
32 0.9870427
33 1.1320528
34 0.9415092
35 0.8847198
36 1.0447899
37 1.1191921
38 1.1303953
39 1.2553456
40 1.1921185
41 0.9842294
42 0.9713984
43 0.9691107
44 1.0560844
45 1.0909978
46 1.2471759
47 0.6725066
48 1.0921047
49 1.0245347
50 0.9713984
51 1.1208443
52 1.1656781
53 1.1656781
54 1.1656781
55 1.2702902
56 1.2030396
57 1.1464743
58 1.0829425
59 1.2204749
60 1.0940337
61 1.0704250
62 0.7322850
63 0.9564538
64 1.0909551
65 1.0909551
66 1.2503890
67 1.0461214
68 1.0816148
69 1.0515558
70 1.0152359
71 1.1058997
72 1.1080347
73 1.1082219
74 1.1806227
75 1.0581667
76 0.9265646
77 1.2019934
78 1.0610660
79 1.0482563
80 1.0415460
81 1.0091994
82 1.0761600
83 1.0909551
84 1.2105119
85 1.2105119
86 1.2105119
87 0.8966755
88 0.8966755
89 1.0386491
90 1.0411398
91 1.1345933
92 1.0934459
93 0.9713984
94 0.9614852
95 1.0673053
96 0.8817309
97 0.8817309
98 1.1235751
99 1.1638100
100 1.1301847
101 1.0098274
102 1.0710290
103 0.9265646
104 0.9415092
105 1.0461214
106 1.0461214
107 1.0461214
108 1.0461214
109 0.9863430
110 0.9938153
111 0.7920633
112 1.0184813
113 0.9265646
114 0.9863430
115 0.8968249
116 1.0504126
117 1.0904570
118 0.8966755
119 0.9564538
120 0.9564538
121 1.1591398
122 1.0162322
123 1.0476158
124 1.0265784
125 0.9713984
126 0.9863430
127 0.8667863
128 0.8667863
129 1.0311768
130 1.0311768
131 1.0845503
132 1.0436430
133 1.0747776
134 1.0219801
135 1.0012876
136 1.1208443
137 1.1208443
138 0.8667863
139 1.2653336
140 1.0704203
141 1.0610660
142 1.1443607
143 0.9427671
144 1.0429403
145 1.1486199
146 1.0719347
147 1.1494021
148 1.0930901
149 0.7322850
150 1.1004789
151 0.8368971
152 1.0760105
153 1.0293274
154 0.9982987
155 1.0252288
156 1.0735198
157 1.1507335
158 0.3909850
159 1.2702902
160 1.2105119
161 1.1694142
162 1.1208443
163 1.0909551
164 1.0436555
165 1.0760105
166 1.0760105
167 1.1836116
168 1.0577449
169 1.1629609
170 1.0461214
171 1.0909666
172 1.1656781
173 1.0461307
174 1.0610660
175 1.1507335
176 1.1574087
177 1.1018375
178 0.9985840
179 1.0461214
180 1.0461214
181 1.0012876
182 0.9863430
183 1.2553456
184 1.0231757
185 0.9713984
186 0.9863430
187 0.9863430
188 0.9863430
189 1.1357889
190 1.1058997
191 0.8966755
192 1.1918311
193 1.0481339
194 1.1656781
195 1.1656781
196 1.1656781
197 1.0931007
198 1.1194993
199 1.0969330
200 1.0252139
201 1.2304380
202 1.0879812
203 1.1152401
204 1.1507459
205 0.8667863
206 0.9564538
207 0.9564538
208 1.0662193
209 1.0610660
210 1.0853603
211 1.0311768
212 1.1537374
213 1.0311768
214 1.0610660
215 0.8966755
216 1.1178554
217 1.0623238
218 1.1557150
219 1.0076924
220 1.2927694
221 1.1507335
222 1.0162322
223 1.0909551
224 1.1208443
225 1.1208443
226 0.9713984
227 1.1195265
228 1.1626892
229 1.0104204
230 1.1272491
231 1.0610660
232 0.8966755
233 1.1088886
234 1.1208443
235 1.1320714
236 1.0199683
237 0.8518417
238 0.9078839
239 0.7920633
240 1.0461214
241 0.9727706
242 1.0845503
243 1.1395251
244 1.0401435
245 0.9265646
246 1.0050237
247 1.1597301
248 1.1208443
249 1.1059246
250 1.2583345
251 0.9265646
252 1.2329287
253 1.2852348
254 1.2404010
255 1.0760404
256 0.9713984
257 1.1477446
258 1.2256059
259 1.1080347
260 0.8779947
261 1.2217203
262 1.1844335
263 1.2503641
264 1.0760105
265 1.0946913
266 1.1208788
267 1.2254564
268 1.0966625
269 0.9190923
270 0.9975514
271 1.0162322
272 1.0536086
273 1.0737114
274 1.0700327
275 1.1408203
276 1.2304878
277 1.1417667
278 0.8219525
279 0.8219525
280 0.9415092
281 0.9415092
282 0.9415092
283 0.9415092
284 0.8518417
285 1.0461214
286 0.8767493
287 1.0516430
288 1.0444775
289 1.0361583
290 1.0118235
291 1.1656781
292 1.1482676
293 1.0866852
294 1.0380743
295 0.9664169
296 1.0845503
297 1.0461214
298 1.1482427
299 1.1955673
300 1.0461214
301 1.0461214
302 1.1413931
303 0.9863430
CNOGpro documentation built on May 2, 2019, 5:57 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Author(s) See Also Examples
Description
Results are printed to stout. The default behavior is to print the HMMtable. If this does not exist, the function will attempt to print the gene table (with copy numbers.)
Usage
1 | printCNOGpro(experiment)
|
Arguments
experiment |
An object of class |
Author(s)
Ola Brynildsrud
See Also
Examples
1 2 3 4 | data(carsonella)
carsonella_normalized <- normalizeGC(carsonella)
carsonella_bootstrapped <- runBootstrap(carsonella_normalized, quantiles=c(0.01,0.99))
printCNOGpro(carsonella_bootstrapped)
|
Example output
Loading required package: seqinr
Normalizing read counts for GC bias...
Overall values for chromosome CP003467 :
Median read count: 66
Median GC percentage: 0.17
Calculating per-read weight based on GC percentage...
Successfully normalized chromosome CP003467
Starting bootstrap analysis for CP003467 - This might take a while...
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Finished bootstrap analysis.
CNOGpro results for C. Carsonella ruddii, artificial example data. Chromosome: CP003467
Type Locus Strand Left Right Length CN_boot Lowerbound
1 CDS CRDC_00005 1 1 1332 1332 0.9692635 0.86784307
2 CDS CRDC_00010 1 1332 2840 1509 1.0283747 0.95924658
3 CDS CRDC_00015 1 2806 3498 693 0.9778032 0.87314839
4 IG 1 3499 3499 1 0.7771187 0.01494459
5 CDS CRDC_00020 1 3500 3730 231 0.9116200 0.81074405
6 IG 1 3731 3735 5 1.0461214 0.01494459
7 CDS CRDC_00030 1 3736 4191 456 0.9564538 0.83091925
8 CDS CRDC_00035 1 4184 4366 183 1.0909551 1.06106595
9 IG 1 4367 4367 1 1.1058997 0.01494459
10 CDS CRDC_00040 1 4368 5813 1446 0.9508496 0.84623746
11 CDS CRDC_00045 1 5810 6562 753 0.9284327 0.84250131
12 CDS CRDC_00050 1 6559 7902 1344 0.9365277 0.87077149
13 CDS CRDC_00055 1 7899 8141 243 1.0797467 0.95645381
14 CDS CRDC_00060 1 8128 9015 888 0.9310480 0.84287492
15 IG 1 9016 9259 244 1.0760105 0.94150922
16 CDS CRDC_00070 -1 9260 9703 444 0.9713984 0.87425856
17 CDS CRDC_00075 -1 9679 11586 1908 0.8944338 0.83762937
18 CDS CRDC_00080 1 11564 13222 1659 0.9730589 0.89666715
19 CDS CRDC_00085 1 13203 13922 720 1.0386491 0.98447492
20 CDS CRDC_00090 -1 13910 14062 153 1.1058997 0.94150922
21 IG 1 14063 14190 128 1.2404010 1.21051186
22 tRNA CRDC_t01077 1 14191 14264 74 1.0087599 0.80700791
23 CDS CRDC_00095 -1 14252 15301 1050 1.0087599 0.91909234
24 CDS CRDC_00100 -1 15301 16245 945 0.9370258 0.84734336
25 CDS CRDC_00105 -1 16242 16943 702 0.9975514 0.92096041
26 CDS CRDC_00110 1 16923 17576 654 0.9756683 0.90094533
27 CDS CRDC_00115 1 17570 18196 627 0.9479140 0.83262720
28 CDS CRDC_00120 1 18171 18716 546 1.1955673 0.96072370
29 CDS CRDC_00125 1 18709 22044 3336 2.0368598 1.90938246
30 CDS CRDC_00130 1 22041 22526 486 0.9464908 0.85928907
31 IG 1 22527 22562 36 0.8368971 0.01494459
32 CDS CRDC_00135 1 22563 24635 2073 0.9122993 0.85250739
33 CDS CRDC_00140 -1 24632 24949 318 0.9938153 0.88546701
34 CDS CRDC_00145 1 24948 25139 192 0.8867124 0.82195250
35 CDS CRDC_00150 1 25114 25554 441 0.7502185 0.59467516
36 CDS CRDC_00155 1 25551 26567 1017 0.9333576 0.83553849
37 CDS CRDC_00160 1 26557 28203 1647 1.0411398 0.96474806
38 CDS CRDC_00165 1 28196 29179 984 1.0366112 0.94694362
39 IG 1 29180 29186 7 1.2553456 0.02988918
40 CDS CRDC_00170 1 29187 30392 1206 1.1047501 1.03002718
41 CDS CRDC_00175 -1 30379 30939 561 0.9543189 0.91588992
42 CDS CRDC_00180 1 30932 31075 144 0.8966755 0.82195250
43 CDS CRDC_00185 1 31072 32277 1206 0.8736838 0.77480806
44 CDS CRDC_00190 1 32274 33623 1350 0.9793689 0.90265329
45 CDS CRDC_00195 1 33620 34285 666 0.9735333 0.84757180
46 CDS CRDC_00200 1 34276 35097 822 1.0594054 0.88837290
47 IG 1 35098 35099 2 0.6725066 0.01494459
48 CDS CRDC_00205 1 35100 36245 1146 1.0173818 0.93115147
49 CDS CRDC_00210 -1 36207 37085 879 0.9581143 0.89333783
50 IG 1 37086 37086 1 0.9713984 0.01494459
51 CDS CRDC_00215 -1 37087 37302 216 1.0050237 0.91535619
52 IG 1 37303 37319 17 1.1656781 0.01494459
53 tRNA CRDC_t01079 1 37320 37390 71 1.1656781 0.01494459
54 tRNA CRDC_t01081 1 37391 37462 72 1.0760105 0.98634300
55 tRNA CRDC_t01083 1 37463 37551 89 1.1283166 0.98634300
56 CDS CRDC_00220 -1 37543 37839 297 1.0274406 0.90041160
57 CDS CRDC_00225 -1 37836 39131 1296 1.0578635 0.98951338
58 CDS CRDC_00230 1 39120 40364 1245 0.9794455 0.86908544
59 CDS CRDC_00235 1 40361 40882 522 1.0610660 0.94150922
60 CDS CRDC_00240 1 40879 41745 867 0.9803652 0.88322532
61 CDS CRDC_00245 1 41742 42482 741 0.9303008 0.78083619
62 IG 1 42483 42484 2 0.7322850 0.01494459
63 tRNA CRDC_t01085 1 42485 42557 73 0.8443694 0.73228495
64 tRNA CRDC_t01087 -1 42558 42630 73 1.0237045 0.95645381
65 IG 1 42631 42659 29 1.0909551 0.02988918
66 CDS CRDC_00255 -1 42660 43106 447 1.1308074 0.99379038
67 CDS CRDC_00260 -1 43096 44019 924 0.9387920 0.83960070
68 CDS CRDC_00265 1 44020 44712 693 1.0031557 0.92467788
69 CDS CRDC_00270 -1 44702 45778 1077 0.9496608 0.87086207
70 CDS CRDC_00275 -1 45765 47120 1356 0.9365277 0.86479366
71 CDS CRDC_00280 -1 47104 47301 198 1.0710290 1.03117677
72 CDS CRDC_00285 1 47291 47836 546 1.0653358 1.02050206
73 CDS CRDC_00290 1 47817 49058 1242 1.0231297 0.95415465
74 CDS CRDC_00295 1 49055 49351 297 1.0573298 0.93777308
75 CDS CRDC_00300 1 49348 49728 381 0.9833541 0.91756799
76 IG 1 49729 49872 144 0.9116200 0.89667545
77 CDS CRDC_00305 1 49873 50445 573 1.0888202 0.98207311
78 CDS CRDC_00310 1 50426 51178 753 0.9732665 0.88918447
79 CDS CRDC_00315 1 51175 52401 1227 0.9585888 0.89131675
80 CDS CRDC_00320 1 52388 53512 1125 0.9955397 0.94725714
81 CDS CRDC_00325 -1 53509 55101 1593 0.9388719 0.87116416
82 IG 1 55102 55107 6 1.0909551 0.01494459
83 CDS CRDC_00330 -1 55108 55392 285 1.0261952 0.95645381
84 IG 1 55393 55523 131 1.1058997 1.03117677
85 tRNA CRDC_t01089 1 55524 55596 73 1.2105119 0.01494459
86 IG 1 55597 55601 5 1.0535937 0.89667545
87 tRNA CRDC_t01091 1 55602 55675 74 0.8966755 0.01494459
88 IG 1 55676 55798 123 0.7696464 0.64261741
89 CDS CRDC_00340 1 55799 56260 462 0.8966755 0.74722954
90 CDS CRDC_00345 1 56260 56724 465 0.9514723 0.84431957
91 CDS CRDC_00350 1 56717 57868 1152 1.0286860 0.92904294
92 CDS CRDC_00355 1 57840 58379 540 1.0187229 0.94898152
93 CDS CRDC_00360 1 58357 58485 129 0.9415092 0.91162004
94 CDS CRDC_00365 1 58482 59249 768 0.8916939 0.81863148
95 CDS CRDC_00370 1 59246 60316 1071 0.9701530 0.87673688
96 IG 1 60317 60320 4 0.8817309 0.01494459
97 tRNA CRDC_t01093 1 60321 60392 72 0.8817309 0.01494459
98 CDS CRDC_00375 -1 60384 61319 936 1.0080806 0.90206909
99 CDS CRDC_00380 -1 61316 62047 732 1.0573298 0.97513455
100 CDS CRDC_00385 -1 62044 62721 678 1.0442533 0.97326648
101 CDS CRDC_00390 -1 62718 63320 603 0.8838658 0.77925367
102 CDS CRDC_00395 -1 63317 63859 543 1.0012876 0.90907946
103 IG 1 63860 63866 7 0.9415092 0.01494459
104 tRNA CRDC_t01095 1 63867 63939 73 0.9340369 0.92656463
105 tRNA CRDC_t01097 1 63940 64010 71 0.9863430 0.92656463
106 IG 1 64011 64012 2 1.0461214 0.01494459
107 tRNA CRDC_t01099 1 64013 64084 72 1.0461214 0.01494459
108 IG 1 64085 64250 166 0.8667863 0.64261741
109 CDS CRDC_00400 -1 64251 64583 333 0.8406332 0.67624274
110 CDS CRDC_00405 1 64584 65036 453 0.9166016 0.82942479
111 IG 1 65037 65097 61 0.7920633 0.01494459
112 CDS CRDC_00415 1 65098 66903 1806 0.9557066 0.88919568
113 IG 1 66904 66953 50 0.9265646 0.01494459
114 CDS CRDC_00420 1 66954 67652 699 0.9377731 0.87610796
115 CDS CRDC_00425 1 67646 68098 453 0.8279303 0.76217413
116 CDS CRDC_00430 1 68091 68642 552 0.9671285 0.86249504
117 CDS CRDC_00435 1 68632 71529 2898 1.0341657 0.97836258
118 IG 1 71530 71533 4 0.8966755 0.01494459
119 tRNA CRDC_t01101 1 71534 71614 81 0.9265646 0.89667545
120 IG 1 71615 71622 8 0.9564538 0.01494459
121 CDS CRDC_00440 1 71623 73176 1554 1.0620000 0.97326648
122 CDS CRDC_00445 1 73163 73357 195 0.8468601 0.71734036
123 CDS CRDC_00450 1 73354 74283 930 1.0042765 0.95344995
124 CDS CRDC_00455 1 74276 75442 1167 0.9645009 0.89552587
125 IG 1 75443 75448 6 0.9863430 0.01494459
126 tRNA CRDC_t01103 1 75449 75522 74 0.9265646 0.86678627
127 tRNA CRDC_t01105 1 75523 75595 73 0.8667863 0.01494459
128 IG 1 75596 75597 2 0.8667863 0.01494459
129 tRNA CRDC_t01107 1 75598 75673 76 0.9489815 0.86678627
130 IG 1 75674 75693 20 1.0311768 0.01494459
131 CDS CRDC_00460 1 75694 76272 579 0.9820731 0.87532604
132 CDS CRDC_00465 1 76253 77326 1074 0.9788707 0.91286542
133 CDS CRDC_00470 1 77326 78420 1095 0.9664169 0.86927703
134 CDS CRDC_00475 1 78417 79682 1266 0.9472571 0.88171936
135 CDS CRDC_00480 1 79669 79878 210 0.8568232 0.71734036
136 IG 1 79879 79924 46 1.0610660 1.00128759
137 tRNA CRDC_t01109 1 79925 80009 85 0.9938153 0.86678627
138 IG 1 80010 80074 65 0.8667863 0.01494459
139 CDS CRDC_00485 1 80075 80572 498 1.0560844 0.85679830
140 CDS CRDC_00490 -1 80573 83617 3045 1.0110950 0.95131661
141 IG 1 83618 83625 8 1.0610660 0.01494459
142 CDS CRDC_00495 1 83626 84984 1359 1.0503912 0.94791405
143 CDS CRDC_00500 1 84977 86014 1038 0.8792401 0.80824083
144 CDS CRDC_00505 1 86007 87371 1365 0.9767358 0.90520454
145 CDS CRDC_00510 1 87355 87909 555 1.0140972 0.88170951
146 CDS CRDC_00515 1 87902 88948 1047 0.9469436 0.82601471
147 CDS CRDC_00520 1 88941 89969 1029 1.0393284 0.90615847
148 CDS CRDC_00525 1 89966 90523 558 0.9692635 0.83894663
149 IG 1 90524 90526 3 0.7322850 0.01494459
150 CDS CRDC_00530 1 90527 91540 1014 0.9944946 0.89528968
151 tRNA CRDC_t01111 1 91520 91598 79 0.8368971 0.01494459
152 IG 1 91599 91608 10 0.9564538 0.83689709
153 CDS CRDC_00535 1 91609 92349 741 0.9396411 0.86303144
154 CDS CRDC_00540 1 92339 92710 372 0.9086311 0.83091925
155 CDS CRDC_00545 -1 92698 93027 330 0.9863430 0.94449814
156 CDS CRDC_00550 -1 93020 93562 543 0.9664169 0.86678627
157 CDS CRDC_00555 -1 93549 94112 564 0.9116200 0.59351375
158 CDS CRDC_00560 -1 94109 95335 1227 0.1253046 0.00000000
159 IG 1 95336 95409 74 1.2404010 1.21051186
160 CDS CRDC_00565 1 95410 95619 210 1.1507335 1.06106595
161 IG 1 95620 95989 370 1.0050237 0.82942479
162 CDS CRDC_00570 -1 95990 96304 315 0.9355314 0.78309656
163 CDS CRDC_00575 -1 96288 96482 195 0.9166016 0.71734036
164 CDS CRDC_00580 -1 96430 96960 531 0.9215831 0.80200147
165 CDS CRDC_00585 -1 96960 97568 609 0.9692635 0.86249504
166 IG 1 97569 97602 34 0.9639261 0.85184168
167 CDS CRDC_00590 -1 97603 98067 465 1.0371546 0.90265329
168 CDS CRDC_00595 -1 98048 99706 1659 0.9938153 0.93652769
169 CDS CRDC_00600 -1 99690 100616 927 1.0434042 0.93743343
170 CDS CRDC_00605 -1 100604 100729 126 0.9863430 0.92656463
171 CDS CRDC_00610 1 100728 101990 1263 1.0346255 0.98287125
172 CDS CRDC_00615 1 101980 102255 276 1.1208443 1.03864906
173 CDS CRDC_00620 1 102242 103780 1539 0.9956834 0.94524537
174 IG 1 103781 103901 121 0.9763799 0.92656463
175 CDS CRDC_00630 1 103902 104132 231 1.0212137 0.92656463
176 CDS CRDC_00635 -1 104116 104940 825 1.0527634 0.94813466
177 CDS CRDC_00640 -1 104933 105976 1044 0.9781914 0.86677268
178 CDS CRDC_00645 -1 105963 106940 978 0.9605296 0.91568225
179 IG 1 106941 106942 2 1.0461214 0.01494459
180 tRNA CRDC_t01113 -1 106943 107015 73 1.0237045 1.00128759
181 IG 1 107016 107107 92 0.9489815 0.89667545
182 CDS CRDC_00650 1 107108 108400 1293 0.9208167 0.84950802
183 CDS CRDC_00655 1 108390 108575 186 1.0311768 0.89667545
184 CDS CRDC_00660 -1 108568 109743 1176 0.9518555 0.88976645
185 IG 1 109744 109778 35 0.9713984 0.01494459
186 tRNA CRDC_t01115 1 109779 109849 71 0.9788707 0.97139841
187 IG 1 109850 109852 3 0.9863430 0.01494459
188 tRNA CRDC_t01117 1 109853 109933 81 0.9863430 0.98634300
189 CDS CRDC_00665 -1 109915 110691 777 1.0442533 0.95639777
190 IG 1 110692 110709 18 1.0012876 0.89667545
191 tRNA CRDC_t01119 -1 110710 110783 74 0.8966755 0.01494459
192 CDS CRDC_00670 -1 110761 111081 321 1.0311768 0.86305012
193 CDS CRDC_00675 1 111075 112472 1398 0.9664169 0.87674933
194 tRNA CRDC_t01121 -1 112438 112510 73 1.1357889 1.10589972
195 IG 1 112511 112515 5 1.1656781 0.01494459
196 tRNA CRDC_t01123 -1 112516 112597 82 1.1656781 0.01494459
197 CDS CRDC_00680 -1 112575 113822 1248 1.0098274 0.91695740
198 CDS CRDC_00685 -1 113819 114811 993 1.0216666 0.92520603
199 CDS CRDC_00690 -1 114804 115706 903 1.0027820 0.88621424
200 CDS CRDC_00695 1 115671 117545 1875 0.9317952 0.84359974
201 CDS CRDC_00700 1 117517 118044 528 1.1258258 1.00377835
202 CDS CRDC_00705 -1 118037 118936 900 0.9639261 0.83689709
203 CDS CRDC_00710 -1 118933 119664 732 1.0199683 0.92469656
204 CDS CRDC_00715 -1 119661 120800 1140 1.0361583 0.91907988
205 IG 1 120801 120807 7 0.8667863 0.01494459
206 rRNA CRDC_r01133 -1 120808 120915 108 0.9116200 0.86678627
207 IG 1 120916 120936 21 0.9564538 0.01494459
208 rRNA CRDC_r01135 -1 120937 123723 2787 1.0177782 0.96676043
209 IG 1 123724 123770 47 1.0760105 0.02988918
210 rRNA CRDC_r01137 -1 123771 125293 1523 1.0031557 0.92935740
211 IG 1 125294 125369 76 1.0087599 0.98634300
212 CDS CRDC_00720 -1 125370 126251 882 1.0461214 0.94298874
213 CDS CRDC_00725 -1 126248 126394 147 0.9415092 0.85184168
214 CDS CRDC_00730 -1 126382 126570 189 0.9963061 0.89667545
215 IG 1 126571 126576 6 0.8966755 0.01494459
216 CDS CRDC_00735 -1 126577 126924 348 1.0042765 0.92354583
217 CDS CRDC_00740 -1 126921 128063 1143 0.9776253 0.89165656
218 CDS CRDC_00745 -1 128060 128869 810 1.0876341 1.01455506
219 CDS CRDC_00750 -1 128862 130169 1308 0.9286996 0.85502274
220 CDS CRDC_00755 -1 130169 131296 1128 1.1656781 1.06852579
221 CDS CRDC_00760 -1 131293 131487 195 1.0511029 0.95645381
222 CDS CRDC_00765 -1 131474 131671 198 0.8916939 0.70239577
223 CDS CRDC_00770 -1 131668 131895 228 1.0112506 0.92656463
224 IG 1 131896 131945 50 1.1058997 1.09095513
225 tRNA CRDC_t01125 1 131946 132018 73 1.0461214 0.97139841
226 IG 1 132019 132022 4 0.9713984 0.02973974
227 CDS CRDC_00775 -1 132023 133018 996 1.0529144 0.99176381
228 CDS CRDC_00780 -1 133019 133471 453 0.9624317 0.78590614
229 CDS CRDC_00785 -1 133392 135068 1677 0.9307159 0.85016456
230 CDS CRDC_00790 -1 135065 135670 606 0.9884779 0.85179898
231 CDS CRDC_00795 -1 135663 135800 138 0.8817309 0.70239577
232 CDS CRDC_00800 -1 135793 135930 138 0.8070079 0.70239577
233 CDS CRDC_00805 -1 135923 138373 2451 1.0090588 0.92058082
234 CDS CRDC_00810 -1 138370 138522 153 1.0511029 0.92656463
235 CDS CRDC_00815 -1 138507 139283 777 1.0237045 0.92467788
236 CDS CRDC_00820 -1 139270 139527 258 0.8630501 0.67250659
237 IG 1 139528 139531 4 0.8518417 0.01494459
238 CDS CRDC_00825 -1 139532 139831 300 0.8256886 0.74722954
239 IG 1 139832 139839 8 0.7920633 0.01494459
240 CDS CRDC_00830 -1 139840 140085 246 0.9016570 0.79206331
241 CDS CRDC_00835 -1 140069 141031 963 0.8980341 0.82466969
242 CDS CRDC_00840 -1 141028 141609 582 0.9948828 0.89667545
243 CDS CRDC_00845 -1 141609 141968 360 0.9900791 0.85931397
244 CDS CRDC_00850 -1 141955 142311 357 0.8608084 0.72923626
245 CDS CRDC_00855 -1 142308 142421 114 0.8667863 0.80700791
246 CDS CRDC_00860 -1 142399 142656 258 0.8929393 0.80700791
247 CDS CRDC_00865 -1 142657 143073 417 1.0939441 1.03416569
248 CDS CRDC_00870 -1 143055 143291 237 1.0859736 1.03117677
249 CDS CRDC_00875 -1 143288 143791 504 0.9913245 0.87425856
250 CDS CRDC_00880 -1 143788 144153 366 1.0999219 0.98030538
251 IG 1 144154 144155 2 0.9265646 0.01494459
252 CDS CRDC_00885 -1 144156 144446 291 1.0610660 0.93403693
253 IG 1 144447 144448 2 1.2852348 0.02988918
254 CDS CRDC_00890 -1 144449 144943 495 1.1258258 0.98634300
255 CDS CRDC_00895 -1 144940 145308 369 0.9444981 0.80700791
256 CDS CRDC_00900 -1 145305 145547 243 0.8717678 0.77711872
257 CDS CRDC_00905 -1 145540 145947 408 1.0102543 0.89966437
258 IG 1 145948 145951 4 1.2404010 0.01494459
259 CDS CRDC_00910 -1 145952 146554 603 0.9906129 0.87746098
260 CDS CRDC_00915 -1 146539 146856 318 0.8406332 0.79206331
261 CDS CRDC_00920 -1 146846 147109 264 1.0124960 0.84436938
262 CDS CRDC_00925 -1 147106 147807 702 1.0816148 0.99751408
263 CDS CRDC_00930 -1 147804 148319 516 1.1706596 1.07100410
264 CDS CRDC_00935 -1 148316 148726 411 1.0192211 0.98036516
265 CDS CRDC_00940 -1 148723 149019 297 1.0124960 0.91909234
266 CDS CRDC_00945 -1 149016 150206 1191 1.0116338 0.91734497
267 IG 1 150207 150225 19 1.2254564 0.02988918
268 CDS CRDC_00950 -1 150226 152262 2037 1.0183671 0.95145805
269 CDS CRDC_00955 -1 152259 152729 471 0.8667863 0.79953561
270 CDS CRDC_00960 -1 152722 153087 366 0.9452454 0.90414775
271 IG 1 153088 153096 9 1.0162322 0.02988918
272 CDS CRDC_00965 -1 153097 156993 3897 0.9934417 0.93365210
273 CDS CRDC_00970 -1 156969 160769 3801 1.0265784 0.97675547
274 CDS CRDC_00975 -1 160766 161110 345 0.9893319 0.89664556
275 CDS CRDC_00980 -1 161091 161525 435 0.9863430 0.88422163
276 CDS CRDC_00985 -1 161522 162094 573 1.0311768 0.85184168
277 CDS CRDC_00990 -1 162087 162500 414 0.9564538 0.76815197
278 IG 1 162501 162519 19 0.8219525 0.01494459
279 tRNA CRDC_t01127 -1 162520 162590 71 0.8219525 0.02973974
280 IG 1 162591 162602 12 0.8817309 0.82195250
281 tRNA CRDC_t01129 -1 162603 162673 71 0.9415092 0.02973974
282 IG 1 162674 162674 1 0.9415092 0.01494459
283 tRNA CRDC_t01131 -1 162675 162755 81 0.8368971 0.73228495
284 IG 1 162756 162812 57 0.7920633 0.73228495
285 CDS CRDC_00995 -1 162813 163088 276 0.9116200 0.83689709
286 CDS CRDC_01000 -1 163055 163558 504 0.8418786 0.81448020
287 CDS CRDC_01005 -1 163551 165356 1806 0.9737581 0.90688497
288 CDS CRDC_01010 -1 165349 166113 765 0.9664169 0.88173086
289 CDS CRDC_01015 1 166090 166839 750 0.8983360 0.75053396
290 CDS CRDC_01020 1 166826 167755 930 0.8623029 0.71282709
291 CDS CRDC_01025 1 167743 167955 213 0.9614353 0.85184168
292 CDS CRDC_01030 1 167946 168410 465 1.0560844 0.94399999
293 CDS CRDC_01035 1 168403 169779 1377 1.0034225 0.91267684
294 CDS CRDC_01040 1 169776 170969 1194 0.9851934 0.93572682
295 CDS CRDC_01045 1 170962 171711 750 0.9016570 0.83854099
296 CDS CRDC_01050 1 171708 172331 624 1.0205021 0.92229475
297 IG 1 172332 172439 108 0.9340369 0.82195250
298 CDS CRDC_01060 1 172440 172988 549 1.0809921 1.02121371
299 IG 1 172989 173016 28 1.0685382 0.94150922
300 CDS CRDC_01065 -1 173017 173220 204 1.0012876 0.94150922
301 IG 1 173221 173286 66 1.0461214 0.01494459
302 CDS CRDC_01070 -1 173287 173964 678 0.9545857 0.75281508
303 IG 1 173965 174014 50 0.8294248 0.67250659
Upperbound
1 1.0589524
2 1.0975027
3 1.0781455
4 0.7771187
5 1.0124960
6 1.0461214
7 1.0610660
8 1.1058997
9 1.1058997
10 1.0582638
11 1.0162322
12 1.0102543
13 1.1619419
14 1.0072654
15 1.2553456
16 1.0635567
17 0.9564688
18 1.0386491
19 1.1002955
20 1.2702902
21 1.2702902
22 1.2105119
23 1.0959616
24 1.0356601
25 1.0834828
26 1.0866852
27 1.0567961
28 1.5115386
29 2.1300569
30 1.0660475
31 0.8368971
32 0.9870427
33 1.1320528
34 0.9415092
35 0.8847198
36 1.0447899
37 1.1191921
38 1.1303953
39 1.2553456
40 1.1921185
41 0.9842294
42 0.9713984
43 0.9691107
44 1.0560844
45 1.0909978
46 1.2471759
47 0.6725066
48 1.0921047
49 1.0245347
50 0.9713984
51 1.1208443
52 1.1656781
53 1.1656781
54 1.1656781
55 1.2702902
56 1.2030396
57 1.1464743
58 1.0829425
59 1.2204749
60 1.0940337
61 1.0704250
62 0.7322850
63 0.9564538
64 1.0909551
65 1.0909551
66 1.2503890
67 1.0461214
68 1.0816148
69 1.0515558
70 1.0152359
71 1.1058997
72 1.1080347
73 1.1082219
74 1.1806227
75 1.0581667
76 0.9265646
77 1.2019934
78 1.0610660
79 1.0482563
80 1.0415460
81 1.0091994
82 1.0761600
83 1.0909551
84 1.2105119
85 1.2105119
86 1.2105119
87 0.8966755
88 0.8966755
89 1.0386491
90 1.0411398
91 1.1345933
92 1.0934459
93 0.9713984
94 0.9614852
95 1.0673053
96 0.8817309
97 0.8817309
98 1.1235751
99 1.1638100
100 1.1301847
101 1.0098274
102 1.0710290
103 0.9265646
104 0.9415092
105 1.0461214
106 1.0461214
107 1.0461214
108 1.0461214
109 0.9863430
110 0.9938153
111 0.7920633
112 1.0184813
113 0.9265646
114 0.9863430
115 0.8968249
116 1.0504126
117 1.0904570
118 0.8966755
119 0.9564538
120 0.9564538
121 1.1591398
122 1.0162322
123 1.0476158
124 1.0265784
125 0.9713984
126 0.9863430
127 0.8667863
128 0.8667863
129 1.0311768
130 1.0311768
131 1.0845503
132 1.0436430
133 1.0747776
134 1.0219801
135 1.0012876
136 1.1208443
137 1.1208443
138 0.8667863
139 1.2653336
140 1.0704203
141 1.0610660
142 1.1443607
143 0.9427671
144 1.0429403
145 1.1486199
146 1.0719347
147 1.1494021
148 1.0930901
149 0.7322850
150 1.1004789
151 0.8368971
152 1.0760105
153 1.0293274
154 0.9982987
155 1.0252288
156 1.0735198
157 1.1507335
158 0.3909850
159 1.2702902
160 1.2105119
161 1.1694142
162 1.1208443
163 1.0909551
164 1.0436555
165 1.0760105
166 1.0760105
167 1.1836116
168 1.0577449
169 1.1629609
170 1.0461214
171 1.0909666
172 1.1656781
173 1.0461307
174 1.0610660
175 1.1507335
176 1.1574087
177 1.1018375
178 0.9985840
179 1.0461214
180 1.0461214
181 1.0012876
182 0.9863430
183 1.2553456
184 1.0231757
185 0.9713984
186 0.9863430
187 0.9863430
188 0.9863430
189 1.1357889
190 1.1058997
191 0.8966755
192 1.1918311
193 1.0481339
194 1.1656781
195 1.1656781
196 1.1656781
197 1.0931007
198 1.1194993
199 1.0969330
200 1.0252139
201 1.2304380
202 1.0879812
203 1.1152401
204 1.1507459
205 0.8667863
206 0.9564538
207 0.9564538
208 1.0662193
209 1.0610660
210 1.0853603
211 1.0311768
212 1.1537374
213 1.0311768
214 1.0610660
215 0.8966755
216 1.1178554
217 1.0623238
218 1.1557150
219 1.0076924
220 1.2927694
221 1.1507335
222 1.0162322
223 1.0909551
224 1.1208443
225 1.1208443
226 0.9713984
227 1.1195265
228 1.1626892
229 1.0104204
230 1.1272491
231 1.0610660
232 0.8966755
233 1.1088886
234 1.1208443
235 1.1320714
236 1.0199683
237 0.8518417
238 0.9078839
239 0.7920633
240 1.0461214
241 0.9727706
242 1.0845503
243 1.1395251
244 1.0401435
245 0.9265646
246 1.0050237
247 1.1597301
248 1.1208443
249 1.1059246
250 1.2583345
251 0.9265646
252 1.2329287
253 1.2852348
254 1.2404010
255 1.0760404
256 0.9713984
257 1.1477446
258 1.2256059
259 1.1080347
260 0.8779947
261 1.2217203
262 1.1844335
263 1.2503641
264 1.0760105
265 1.0946913
266 1.1208788
267 1.2254564
268 1.0966625
269 0.9190923
270 0.9975514
271 1.0162322
272 1.0536086
273 1.0737114
274 1.0700327
275 1.1408203
276 1.2304878
277 1.1417667
278 0.8219525
279 0.8219525
280 0.9415092
281 0.9415092
282 0.9415092
283 0.9415092
284 0.8518417
285 1.0461214
286 0.8767493
287 1.0516430
288 1.0444775
289 1.0361583
290 1.0118235
291 1.1656781
292 1.1482676
293 1.0866852
294 1.0380743
295 0.9664169
296 1.0845503
297 1.0461214
298 1.1482427
299 1.1955673
300 1.0461214
301 1.0461214
302 1.1413931
303 0.9863430
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