runBootstrap: Gene copy numbers with confidence intervals through...
In CNOGpro: Copy Numbers of Genes in prokaryotes
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
For each genetic element in the gene table of a CNOGpro object,
sample repeatedly from the read observations associated with that gene
while replacing the observations.
Usage
1
runBootstrap(experiment, replicates = 1000, quantiles = c(0.025, 0.975))
Arguments
experiment
An object of class CNOGpro
replicates
The (integer) number of resampling experiments per genetic element.
(That is, the number of bootstrap samples.)
quantiles
The quantiles of the distribution of mean copy numbers for which the
mean is returned. (Given as c(lower, upper))
Details
Implements the theory that since the read counts from each genetic element
come from a (overdispersed) Poisson distribution with rate parameter
lambda (=mean), this lambda can be inferred by simply taking the mean of
the observations from that genetic element. A confidence interval is then
constructed around the mean by random resampling with replacement. For each
replicate and genetic element, the same number of samples is taken as there
are read count observations associated with that particular genetic element.
The observations of means are then sorted and the given lower and upper
quantiles are returned.
Value
An object of class CNOGpro, with proposed copy number (floating point)
and the associated confidence interval for each genetic element in the table
of genes.
Author(s)
Ola Brynildsrud
Examples
1
2
3
4
data(carsonella)
carsonella_normalized <- normalizeGC(carsonella)
carsonella_bootstrapped <- runBootstrap(carsonella, replicates=500)
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 0.9738434 0.89239711
2 CDS CRDC_00010 1 1332 2840 1509 1.0299858 0.97690330
3 CDS CRDC_00015 1 2806 3498 693 0.9621360 0.88976294
4 IG 1 3499 3499 1 0.8046182 0.01490034
5 CDS CRDC_00020 1 3500 3730 231 0.9126456 0.83069375
6 IG 1 3731 3735 5 1.0281232 0.03687833
7 CDS CRDC_00030 1 3736 4191 456 0.9536215 0.83441884
8 CDS CRDC_00035 1 4184 4366 183 1.0877246 1.04302354
9 IG 1 4367 4367 1 1.1324256 0.02980067
10 CDS CRDC_00040 1 4368 5813 1446 0.9638655 0.88843255
11 CDS CRDC_00045 1 5810 6562 753 0.9405837 0.86696676
12 CDS CRDC_00050 1 6559 7902 1344 0.9675285 0.90395374
13 CDS CRDC_00055 1 7899 8141 243 1.0765493 0.94244627
14 CDS CRDC_00060 1 8128 9015 888 0.9104106 0.83590887
15 IG 1 9016 9259 244 1.0579239 0.90892052
16 CDS CRDC_00070 -1 9260 9703 444 0.9784554 0.89650357
17 CDS CRDC_00075 -1 9679 11586 1908 0.8888051 0.83739890
18 CDS CRDC_00080 1 11564 13222 1659 0.9652107 0.90600253
19 CDS CRDC_00085 1 13203 13922 720 1.0318483 0.97597203
20 CDS CRDC_00090 -1 13910 14062 153 1.0430235 0.90892052
21 IG 1 14063 14190 128 1.2069272 1.17712657
22 tRNA CRDC_t01077 1 14191 14264 74 1.0579239 0.87911984
23 CDS CRDC_00095 -1 14252 15301 1050 1.0256398 0.94551947
24 CDS CRDC_00100 -1 15301 16245 945 0.9506415 0.86421951
25 CDS CRDC_00105 -1 16242 16943 702 0.9908724 0.92186518
26 CDS CRDC_00110 1 16923 17576 654 0.9600074 0.88337708
27 CDS CRDC_00115 1 17570 18196 627 0.9259495 0.83867607
28 CDS CRDC_00120 1 18171 18716 546 1.2090559 0.97458843
29 CDS CRDC_00125 1 18709 22044 3336 2.0509875 1.95653468
30 CDS CRDC_00130 1 22041 22526 486 0.9312710 0.84435239
31 IG 1 22527 22562 36 0.8344188 0.02980067
32 CDS CRDC_00135 1 22563 24635 2073 0.9089205 0.85267175
33 CDS CRDC_00140 -1 24632 24949 318 0.9945975 0.90147035
34 CDS CRDC_00145 1 24948 25139 192 0.8791198 0.80461816
35 CDS CRDC_00150 1 25114 25554 441 0.7450168 0.60182459
36 CDS CRDC_00155 1 25551 26567 1017 0.9184025 0.82764596
37 CDS CRDC_00160 1 26557 28203 1647 1.0546127 0.99540455
38 CDS CRDC_00165 1 28196 29179 984 1.0389598 0.95362153
39 IG 1 29180 29186 7 1.2516283 0.04470101
40 CDS CRDC_00170 1 29187 30392 1206 1.1095020 1.05098949
41 CDS CRDC_00175 -1 30379 30939 561 0.9408498 0.90993161
42 CDS CRDC_00180 1 30932 31075 144 0.8716697 0.80461816
43 CDS CRDC_00185 1 31072 32277 1206 0.8676580 0.79135113
44 CDS CRDC_00190 1 32274 33623 1350 0.9764687 0.90839901
45 CDS CRDC_00195 1 33620 34285 666 0.9621360 0.85346998
46 CDS CRDC_00200 1 34276 35097 822 1.0314344 0.89402018
47 IG 1 35098 35099 2 0.6854155 0.02980067
48 CDS CRDC_00205 1 35100 36245 1146 1.0132229 0.93986737
49 CDS CRDC_00210 -1 36207 37085 879 0.9503103 0.90229815
50 IG 1 37086 37086 1 0.9238209 0.02980067
51 CDS CRDC_00215 -1 37087 37302 216 0.9983225 0.92382085
52 IG 1 37303 37319 17 1.2069272 0.04470101
53 tRNA CRDC_t01079 1 37320 37390 71 1.2069272 0.03687833
54 tRNA CRDC_t01081 1 37391 37462 72 1.1920269 1.17712657
55 tRNA CRDC_t01083 1 37463 37551 89 1.2516283 1.17712657
56 CDS CRDC_00220 -1 37543 37839 297 1.0281232 0.90892052
57 CDS CRDC_00225 -1 37836 39131 1296 1.0526023 0.99350653
58 CDS CRDC_00230 1 39120 40364 1245 0.9547677 0.87562400
59 CDS CRDC_00235 1 40361 40882 522 1.0380568 0.94853058
60 CDS CRDC_00240 1 40879 41745 867 0.9536215 0.87464974
61 CDS CRDC_00245 1 41742 42482 741 0.9089205 0.78040512
62 IG 1 42483 42484 2 0.7301165 0.02980067
63 tRNA CRDC_t01085 1 42485 42557 73 0.8418690 0.73011648
64 tRNA CRDC_t01087 -1 42558 42630 73 1.0206730 0.95362153
65 IG 1 42631 42659 29 1.0877246 0.05960135
66 CDS CRDC_00255 -1 42660 43106 447 1.1200086 0.97845542
67 CDS CRDC_00260 -1 43096 44019 924 0.9292392 0.84390087
68 CDS CRDC_00265 1 44020 44712 693 1.0169480 0.94333098
69 CDS CRDC_00270 -1 44702 45778 1077 0.9414303 0.86686093
70 CDS CRDC_00275 -1 45765 47120 1356 0.9337544 0.87017964
71 CDS CRDC_00280 -1 47104 47301 198 1.0529571 0.98342220
72 CDS CRDC_00285 1 47291 47836 546 1.0494094 1.00784811
73 CDS CRDC_00290 1 47817 49058 1242 1.0304156 0.96393714
74 CDS CRDC_00295 1 49055 49351 297 1.0467486 0.93872119
75 CDS CRDC_00300 1 49348 49728 381 0.9804421 0.91786072
76 IG 1 49729 49872 144 0.9238209 0.89402018
77 CDS CRDC_00305 1 49873 50445 573 1.0877246 0.98970163
78 CDS CRDC_00310 1 50426 51178 753 0.9685219 0.89402018
79 CDS CRDC_00315 1 51175 52401 1227 0.9461714 0.88651680
80 CDS CRDC_00320 1 52388 53512 1125 0.9948840 0.94215973
81 CDS CRDC_00325 -1 53509 55101 1593 0.9667689 0.91242648
82 IG 1 55102 55107 6 1.0728242 0.04470101
83 CDS CRDC_00330 -1 55108 55392 285 1.0380568 0.99832254
84 IG 1 55393 55523 131 1.1075917 1.04302354
85 tRNA CRDC_t01089 1 55524 55596 73 1.2069272 0.03687833
86 IG 1 55597 55601 5 1.0579239 0.90892052
87 tRNA CRDC_t01091 1 55602 55675 74 0.9089205 0.03687833
88 IG 1 55676 55798 123 0.7599172 0.61091379
89 CDS CRDC_00340 1 55799 56260 462 0.8691863 0.73992587
90 CDS CRDC_00345 1 56260 56724 465 0.9511381 0.84186900
91 CDS CRDC_00350 1 56717 57868 1152 1.0368151 0.94787869
92 CDS CRDC_00355 1 57840 58379 540 0.9685219 0.90643713
93 CDS CRDC_00360 1 58357 58485 129 0.9238209 0.89402018
94 CDS CRDC_00365 1 58482 59249 768 0.8824310 0.83276324
95 CDS CRDC_00370 1 59246 60316 1071 0.9486547 0.88160323
96 IG 1 60317 60320 4 0.8791198 0.01490034
97 tRNA CRDC_t01093 1 60321 60392 72 0.8791198 0.02980067
98 CDS CRDC_00375 -1 60384 61319 936 0.9915497 0.90214764
99 CDS CRDC_00380 -1 61316 62047 732 1.0579239 0.98155966
100 CDS CRDC_00385 -1 62044 62721 678 1.0523363 1.00018508
101 CDS CRDC_00390 -1 62718 63320 603 0.8684767 0.78971783
102 CDS CRDC_00395 -1 63317 63859 543 0.9908724 0.90892052
103 IG 1 63860 63866 7 0.9387212 0.03687833
104 tRNA CRDC_t01095 1 63867 63939 73 0.9312710 0.92382085
105 tRNA CRDC_t01097 1 63940 64010 71 1.0579239 0.92382085
106 IG 1 64011 64012 2 1.1920269 0.03687833
107 tRNA CRDC_t01099 1 64013 64084 72 1.1920269 0.02980067
108 IG 1 64085 64250 166 0.9188541 0.64071446
109 CDS CRDC_00400 -1 64251 64583 333 0.8381439 0.70031581
110 CDS CRDC_00405 1 64584 65036 453 0.9263042 0.84931917
111 IG 1 65037 65097 61 0.7748175 0.02980067
112 CDS CRDC_00415 1 65098 66903 1806 0.9774621 0.91935075
113 IG 1 66904 66953 50 0.9238209 0.02980067
114 CDS CRDC_00420 1 66954 67652 699 0.9349961 0.88098239
115 CDS CRDC_00425 1 67646 68098 453 0.8493192 0.78375769
116 CDS CRDC_00430 1 68091 68642 552 0.9876794 0.90029961
117 CDS CRDC_00435 1 68632 71529 2898 1.0385534 0.99503204
118 IG 1 71530 71533 4 0.8940202 0.02980067
119 tRNA CRDC_t01101 1 71534 71614 81 0.9014703 0.89402018
120 IG 1 71615 71622 8 0.9089205 0.02980067
121 CDS CRDC_00440 1 71623 73176 1554 1.0560613 0.97131568
122 CDS CRDC_00445 1 73163 73357 195 0.8244853 0.71521614
123 CDS CRDC_00450 1 73354 74283 930 0.9789521 0.93574112
124 CDS CRDC_00455 1 74276 75442 1167 0.9582062 0.90083995
125 IG 1 75443 75448 6 0.9834222 0.02980067
126 tRNA CRDC_t01103 1 75449 75522 74 0.9834222 0.98342220
127 tRNA CRDC_t01105 1 75523 75595 73 0.9834222 0.02980067
128 IG 1 75596 75597 2 0.9834222 0.04470101
129 tRNA CRDC_t01107 1 75598 75673 76 1.0355734 0.98342220
130 IG 1 75674 75693 20 1.0877246 0.02980067
131 CDS CRDC_00460 1 75694 76272 579 1.0153515 0.93233533
132 CDS CRDC_00465 1 76253 77326 1074 0.9995642 0.94551947
133 CDS CRDC_00470 1 77326 78420 1095 0.9660385 0.88715982
134 CDS CRDC_00475 1 78417 79682 1266 0.9295518 0.87109659
135 CDS CRDC_00480 1 79669 79878 210 0.7946846 0.65561480
136 IG 1 79879 79924 46 0.9834222 0.92382085
137 tRNA CRDC_t01109 1 79925 80009 85 0.9536215 0.86421951
138 IG 1 80010 80074 65 0.8642195 0.02980067
139 CDS CRDC_00485 1 80075 80572 498 1.0554405 0.89402018
140 CDS CRDC_00490 -1 80573 83617 3045 1.0225356 0.96619369
141 IG 1 83618 83625 8 1.0877246 0.02980067
142 CDS CRDC_00495 1 83626 84984 1359 1.0483451 0.96740434
143 CDS CRDC_00500 1 84977 86014 1038 0.8853283 0.83128356
144 CDS CRDC_00505 1 86007 87371 1365 0.9791650 0.92539071
145 CDS CRDC_00510 1 87355 87909 555 1.0025798 0.87464974
146 CDS CRDC_00515 1 87902 88948 1047 0.9739402 0.87641069
147 CDS CRDC_00520 1 88941 89969 1029 1.0470873 0.94613749
148 CDS CRDC_00525 1 89966 90523 558 0.9536215 0.84506193
149 IG 1 90524 90526 3 0.7003158 0.02980067
150 CDS CRDC_00530 1 90527 91540 1014 0.9766493 0.89595045
151 tRNA CRDC_t01111 1 91520 91598 79 0.7897178 0.02980067
152 IG 1 91599 91608 10 0.8940202 0.78971783
153 CDS CRDC_00535 1 91609 92349 741 0.9163707 0.85765405
154 CDS CRDC_00540 1 92339 92710 372 0.8850800 0.82249857
155 CDS CRDC_00545 -1 92698 93027 330 0.9625617 0.91190058
156 CDS CRDC_00550 -1 93020 93562 543 0.9511381 0.87284929
157 CDS CRDC_00555 -1 93549 94112 564 0.9153064 0.63198712
158 CDS CRDC_00560 -1 94109 95335 1227 0.1272259 0.00000000
159 IG 1 95336 95409 74 1.2665286 1.22182758
160 CDS CRDC_00565 1 95410 95619 210 1.1522927 1.04302354
161 IG 1 95620 95989 370 0.9871473 0.81206833
162 CDS CRDC_00570 -1 95990 96304 315 0.9089205 0.75380802
163 CDS CRDC_00575 -1 96288 96482 195 0.9039537 0.68541547
164 CDS CRDC_00580 -1 96430 96960 531 0.9014703 0.80201060
165 CDS CRDC_00585 -1 96960 97568 609 0.9557501 0.85996227
166 IG 1 97569 97602 34 0.9312710 0.80461816
167 CDS CRDC_00590 -1 97603 98067 465 1.0370634 0.89998032
168 CDS CRDC_00595 -1 98048 99706 1659 0.9834222 0.92713204
169 CDS CRDC_00600 -1 99690 100616 927 1.0470873 0.96303583
170 CDS CRDC_00605 -1 100604 100729 126 0.9759720 0.92382085
171 CDS CRDC_00610 1 100728 101990 1263 1.0201000 0.97135866
172 CDS CRDC_00615 1 101980 102255 276 1.1100751 1.03184829
173 CDS CRDC_00620 1 102242 103780 1539 0.9824909 0.94710263
174 IG 1 103781 103901 121 0.9387212 0.90892052
175 CDS CRDC_00630 1 103902 104132 231 1.0032893 0.90892052
176 CDS CRDC_00635 -1 104116 104940 825 1.0662018 0.96843908
177 CDS CRDC_00640 -1 104933 105976 1044 0.9766493 0.87705412
178 CDS CRDC_00645 -1 105963 106940 978 0.9414303 0.89943849
179 IG 1 106941 106942 2 1.0728242 0.05177867
180 tRNA CRDC_t01113 -1 106943 107015 73 1.0355734 0.99832254
181 IG 1 107016 107107 92 0.9461714 0.89402018
182 CDS CRDC_00650 1 107108 108400 1293 0.8917278 0.83098030
183 CDS CRDC_00655 1 108390 108575 186 1.0082561 0.86421951
184 CDS CRDC_00660 -1 108568 109743 1176 0.9765451 0.91115557
185 IG 1 109744 109778 35 1.0132229 0.02980067
186 tRNA CRDC_t01115 1 109779 109849 71 0.9461714 0.87911984
187 IG 1 109850 109852 3 0.8791198 0.02980067
188 tRNA CRDC_t01117 1 109853 109933 81 0.9312710 0.87911984
189 CDS CRDC_00665 -1 109915 110691 777 1.0579239 0.98616945
190 IG 1 110692 110709 18 1.0281232 0.95362153
191 tRNA CRDC_t01119 -1 110710 110783 74 0.9536215 0.02980067
192 CDS CRDC_00670 -1 110761 111081 321 1.0355734 0.91637069
193 CDS CRDC_00675 1 111075 112472 1398 0.9695152 0.89548538
194 tRNA CRDC_t01121 -1 112438 112510 73 1.1920269 1.14732590
195 IG 1 112511 112515 5 1.2367279 0.05960135
196 tRNA CRDC_t01123 -1 112516 112597 82 1.2367279 0.04470101
197 CDS CRDC_00680 -1 112575 113822 1248 1.0206730 0.95681446
198 CDS CRDC_00685 -1 113819 114811 993 0.9915497 0.90072533
199 CDS CRDC_00690 -1 114804 115706 903 1.0102428 0.90743048
200 CDS CRDC_00695 1 115671 117545 1875 0.9104106 0.83700777
201 CDS CRDC_00700 1 117517 118044 528 1.1349090 1.05047371
202 CDS CRDC_00705 -1 118037 118936 900 0.9640518 0.85747711
203 CDS CRDC_00710 -1 118933 119664 732 1.0039102 0.90608014
204 CDS CRDC_00715 -1 119661 120800 1140 1.0628907 0.96976356
205 IG 1 120801 120807 7 0.9089205 0.02980067
206 rRNA CRDC_r01133 -1 120808 120915 108 0.9461714 0.90892052
207 IG 1 120916 120936 21 0.9834222 0.04470101
208 rRNA CRDC_r01135 -1 120937 123723 2787 1.0836141 1.03631839
209 IG 1 123724 123770 47 1.0281232 0.02980067
210 rRNA CRDC_r01137 -1 123771 125293 1523 1.0551301 0.99969616
211 IG 1 125294 125369 76 1.0877246 0.96852186
212 CDS CRDC_00720 -1 125370 126251 882 1.0385534 0.95879939
213 CDS CRDC_00725 -1 126248 126394 147 0.9610717 0.89402018
214 CDS CRDC_00730 -1 126382 126570 189 0.9834222 0.92878763
215 IG 1 126571 126576 6 0.8791198 0.02980067
216 CDS CRDC_00735 -1 126577 126924 348 0.9983225 0.91488065
217 CDS CRDC_00740 -1 126921 128063 1143 0.9672802 0.89402018
218 CDS CRDC_00745 -1 128060 128869 810 1.0794466 1.01069809
219 CDS CRDC_00750 -1 128862 130169 1308 0.9227565 0.85985584
220 CDS CRDC_00755 -1 130169 131296 1128 1.1498093 1.05910349
221 CDS CRDC_00760 -1 131293 131487 195 1.0479903 0.95362153
222 CDS CRDC_00765 -1 131474 131671 198 0.8890534 0.70031581
223 CDS CRDC_00770 -1 131668 131895 228 1.0082561 0.92382085
224 IG 1 131896 131945 50 1.1398757 1.08772455
225 tRNA CRDC_t01125 1 131946 132018 73 1.1026249 1.01322287
226 IG 1 132019 132022 4 1.0132229 0.02980067
227 CDS CRDC_00775 -1 132023 133018 996 1.0863700 1.03147578
228 CDS CRDC_00780 -1 133019 133471 453 0.9387212 0.78658876
229 CDS CRDC_00785 -1 133392 135068 1677 0.9486547 0.87289068
230 CDS CRDC_00790 -1 135065 135670 606 0.9834222 0.87273399
231 CDS CRDC_00795 -1 135663 135800 138 0.8791198 0.70031581
232 CDS CRDC_00800 -1 135793 135930 138 0.7897178 0.70031581
233 CDS CRDC_00805 -1 135923 138373 2451 1.0048787 0.93332727
234 CDS CRDC_00810 -1 138370 138522 153 1.0529571 0.95362153
235 CDS CRDC_00815 -1 138507 139283 777 0.9834222 0.82962279
236 CDS CRDC_00820 -1 139270 139527 258 0.8791198 0.69659072
237 IG 1 139528 139531 4 0.8940202 0.02980067
238 CDS CRDC_00825 -1 139532 139831 300 0.8493192 0.77481749
239 IG 1 139832 139839 8 0.8046182 0.02980067
240 CDS CRDC_00830 -1 139840 140085 246 0.8940202 0.80461816
241 CDS CRDC_00835 -1 140069 141031 963 0.9035022 0.83848256
242 CDS CRDC_00840 -1 141028 141609 582 1.0047084 0.93233533
243 CDS CRDC_00845 -1 141609 141968 360 1.0020476 0.86421951
244 CDS CRDC_00850 -1 141955 142311 357 0.8552793 0.73011648
245 CDS CRDC_00855 -1 142308 142421 114 0.8567693 0.78971783
246 CDS CRDC_00860 -1 142399 142656 258 0.8977453 0.81206833
247 CDS CRDC_00865 -1 142657 143073 417 1.0996448 1.04004348
248 CDS CRDC_00870 -1 143055 143291 237 1.0877246 1.02812321
249 CDS CRDC_00875 -1 143288 143791 504 0.9859056 0.89755901
250 CDS CRDC_00880 -1 143788 144153 366 1.0907046 1.00428267
251 IG 1 144154 144155 2 0.9685219 0.04470101
252 CDS CRDC_00885 -1 144156 144446 291 1.0541988 0.96107169
253 IG 1 144447 144448 2 1.2665286 0.02980067
254 CDS CRDC_00890 -1 144449 144943 495 1.1249754 1.01570626
255 CDS CRDC_00895 -1 144940 145308 369 0.9655418 0.85527931
256 CDS CRDC_00900 -1 145305 145547 243 0.8791198 0.80461816
257 CDS CRDC_00905 -1 145540 145947 408 1.0102428 0.90296038
258 IG 1 145948 145951 4 1.2367279 0.04470101
259 CDS CRDC_00910 -1 145952 146554 603 0.9898081 0.89077404
260 CDS CRDC_00915 -1 146539 146856 318 0.8381439 0.79716799
261 CDS CRDC_00920 -1 146846 147109 264 1.0243981 0.85676934
262 CDS CRDC_00925 -1 147106 147807 702 1.0877246 1.02253558
263 CDS CRDC_00930 -1 147804 148319 516 1.1820934 1.08027439
264 CDS CRDC_00935 -1 148316 148726 411 0.9893823 0.93872119
265 CDS CRDC_00940 -1 148723 149019 297 1.0243981 0.96852186
266 CDS CRDC_00945 -1 149016 150206 1191 1.0327079 0.94089893
267 IG 1 150207 150225 19 1.2218276 0.02980067
268 CDS CRDC_00950 -1 150226 152262 2037 1.0259946 0.97206956
269 CDS CRDC_00955 -1 152259 152729 471 0.8691863 0.80461816
270 CDS CRDC_00960 -1 152722 153087 366 0.9163707 0.86794459
271 IG 1 153088 153096 9 0.9685219 0.03687833
272 CDS CRDC_00965 -1 153097 156993 3897 0.9942249 0.93517305
273 CDS CRDC_00970 -1 156969 160769 3801 1.0204820 0.98207544
274 CDS CRDC_00975 -1 160766 161110 345 0.9834222 0.90437591
275 CDS CRDC_00980 -1 161091 161525 435 0.9585883 0.85676934
276 CDS CRDC_00985 -1 161522 162094 573 1.0231564 0.87663646
277 CDS CRDC_00990 -1 162087 162500 414 0.9417013 0.76587729
278 IG 1 162501 162519 19 0.8642195 0.04470101
279 tRNA CRDC_t01127 -1 162520 162590 71 0.8642195 0.04470101
280 IG 1 162591 162602 12 0.9312710 0.86421951
281 tRNA CRDC_t01129 -1 162603 162673 71 0.9983225 0.02980067
282 IG 1 162674 162674 1 0.9983225 0.02980067
283 tRNA CRDC_t01131 -1 162675 162755 81 0.8716697 0.74501682
284 IG 1 162756 162812 57 0.7897178 0.74501682
285 CDS CRDC_00995 -1 162813 163088 276 0.8940202 0.81951850
286 CDS CRDC_01000 -1 163055 163558 504 0.8369022 0.81703511
287 CDS CRDC_01005 -1 163551 165356 1806 0.9849907 0.92184068
288 CDS CRDC_01010 -1 165349 166113 765 0.9652107 0.89646218
289 CDS CRDC_01015 1 166090 166839 750 0.8956758 0.76653953
290 CDS CRDC_01020 1 166826 167755 930 0.8478291 0.73082425
291 CDS CRDC_01025 1 167743 167955 213 0.9486547 0.83441884
292 CDS CRDC_01030 1 167946 168410 465 1.0455069 0.97218486
293 CDS CRDC_01035 1 168403 169779 1377 1.0153515 0.93334643
294 CDS CRDC_01040 1 169776 170969 1194 0.9834222 0.93353473
295 CDS CRDC_01045 1 170962 171711 750 0.9072649 0.83938561
296 CDS CRDC_01050 1 171708 172331 624 1.0345091 0.95888986
297 IG 1 172332 172439 108 0.9014703 0.81951850
298 CDS CRDC_01060 1 172440 172988 549 1.0181897 0.96107169
299 IG 1 172989 173016 28 1.0430235 0.95362153
300 CDS CRDC_01065 -1 173017 173220 204 1.0430235 0.95362153
301 IG 1 173221 173286 66 1.0877246 0.02197800
302 CDS CRDC_01070 -1 173287 173964 678 0.9443088 0.77756474
303 IG 1 173965 174014 50 0.3650582 0.08940202
Upperbound
1 1.0531611
2 1.0835571
3 1.0366377
4 0.7897178
5 0.9983225
6 1.0132229
7 1.0460036
8 1.1324256
9 1.0877246
10 1.0453750
11 1.0188105
12 1.0276514
13 1.1771266
14 0.9775366
15 1.2069272
16 1.0628907
17 0.9439363
18 1.0281232
19 1.0933122
20 1.1771266
21 1.2367279
22 1.2367279
23 1.0977202
24 1.0461526
25 1.0682144
26 1.0569128
27 1.0174801
28 1.4900336
29 2.1287870
30 1.0206730
31 0.8195185
32 0.9726195
33 1.1063500
34 0.9387212
35 0.8612394
36 1.0193523
37 1.1117307
38 1.1242981
39 1.2218276
40 1.1719974
41 0.9706505
42 0.9387212
43 0.9479479
44 1.0544720
45 1.0803276
46 1.1597842
47 0.6705151
48 1.0699874
49 1.0148785
50 0.9089205
51 1.1361506
52 1.1920269
53 1.1920269
54 1.2069272
55 1.3261299
56 1.2292777
57 1.1196538
58 1.0413329
59 1.1287626
60 1.0385534
61 1.0226287
62 0.7152161
63 0.9536215
64 1.0877246
65 1.0579239
66 1.2342445
67 1.0118683
68 1.0765493
69 1.0403821
70 0.9978507
71 1.1026249
72 1.0919818
73 1.1095020
74 1.1645544
75 1.0430235
76 0.9536215
77 1.1707407
78 1.0504737
79 1.0153515
80 1.0585256
81 1.0185256
82 1.0579239
83 1.0728242
84 1.2069272
85 1.1771266
86 1.2069272
87 0.8940202
88 0.9089205
89 0.9747924
90 1.0355734
91 1.1243856
92 1.0306066
93 0.9536215
94 0.9320988
95 1.0163582
96 0.8642195
97 0.8642195
98 1.0687605
99 1.1473259
100 1.1119376
101 0.9526104
102 1.0592277
103 0.9238209
104 0.9387212
105 1.1920269
106 1.1771266
107 1.1473259
108 1.1920269
109 0.9759720
110 1.0008059
111 0.7748175
112 1.0367468
113 0.9089205
114 0.9759720
115 0.9178607
116 1.0643097
117 1.0820252
118 0.8791198
119 0.9089205
120 0.8940202
121 1.1450210
122 0.9536215
123 1.0281232
124 1.0097843
125 0.9685219
126 0.9834222
127 0.9685219
128 0.9685219
129 1.0877246
130 1.0728242
131 1.0909707
132 1.0474005
133 1.0610592
134 0.9954857
135 0.8840866
136 1.0430235
137 1.0430235
138 0.8493192
139 1.2441781
140 1.0689012
141 1.0806469
142 1.1228468
143 0.9418565
144 1.0286820
145 1.1112458
146 1.0877246
147 1.1527442
148 1.0675559
149 0.6854155
150 1.0775991
151 0.7748175
152 0.9983225
153 0.9796971
154 0.9686709
155 1.0132229
156 1.0355734
157 1.1143855
158 0.3427077
159 1.3112296
160 1.2171091
161 1.1622262
162 1.0670131
163 1.0728242
164 1.0095599
165 1.0356266
166 1.0579239
167 1.1565641
168 1.0438513
169 1.1446845
170 1.0281232
171 1.0706465
172 1.1622262
173 1.0244447
174 0.9834222
175 1.1771266
176 1.1630954
177 1.0986289
178 0.9807130
179 1.0579239
180 1.0728242
181 0.9983225
182 0.9450538
183 1.1920269
184 1.0424791
185 0.9983225
186 1.0132229
187 0.8642195
188 0.9834222
189 1.1212503
190 1.1026249
191 0.9387212
192 1.1606431
193 1.0520134
194 1.2367279
195 1.2296503
196 1.2069272
197 1.0877778
198 1.0803082
199 1.1116396
200 0.9811871
201 1.2181646
202 1.0818389
203 1.0989929
204 1.1554280
205 0.8940202
206 0.9834222
207 0.9685219
208 1.1425090
209 1.0132229
210 1.1147780
211 1.2069272
212 1.1273967
213 1.0281232
214 1.0430235
215 0.8642195
216 1.1115651
217 1.0411920
218 1.1399171
219 0.9844865
220 1.2466615
221 1.1324256
222 0.9933558
223 1.0877246
224 1.1920269
225 1.1920269
226 0.9834222
227 1.1500351
228 1.0907046
229 1.0306066
230 1.0973566
231 1.0579239
232 0.8493192
233 1.0859663
234 1.1026249
235 1.1231129
236 1.0057727
237 0.8791198
238 0.9238209
239 0.7897178
240 1.0430235
241 0.9698764
242 1.0867135
243 1.1287005
244 1.0191830
245 0.9238209
246 0.9908724
247 1.1562661
248 1.1175252
249 1.0853653
250 1.1920269
251 0.9536215
252 1.1920269
253 1.2367279
254 1.2219518
255 1.0758043
256 0.9983225
257 1.1310100
258 1.2218276
259 1.1004963
260 0.8716697
261 1.1920269
262 1.1491884
263 1.2541116
264 1.0489837
265 1.0839995
266 1.1175252
267 1.1771266
268 1.0834673
269 0.9238209
270 0.9573466
271 0.9536215
272 1.0424927
273 1.0581436
274 1.0668641
275 1.0877246
276 1.1833971
277 1.0758043
278 0.8493192
279 0.8493192
280 0.9983225
281 0.9685219
282 0.9536215
283 0.9983225
284 0.8344188
285 1.0281232
286 0.8592527
287 1.0516501
288 1.0356148
289 1.0223700
290 0.9603639
291 1.1622262
292 1.1200086
293 1.1026249
294 1.0287250
295 0.9760134
296 1.1090107
297 0.9834222
298 1.0691612
299 1.1324256
300 1.0877246
301 1.0728242
302 1.0858620
303 0.6407145
CNOGpro documentation built on May 2, 2019, 5:57 a.m.
R Package Documentation
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Description Usage Arguments Details Value Author(s) Examples
Description
For each genetic element in the gene table of a CNOGpro object,
sample repeatedly from the read observations associated with that gene
while replacing the observations.
Usage
1 | runBootstrap(experiment, replicates = 1000, quantiles = c(0.025, 0.975))
|
Arguments
experiment |
An object of class |
replicates |
The (integer) number of resampling experiments per genetic element. (That is, the number of bootstrap samples.) |
quantiles |
The quantiles of the distribution of mean copy numbers for which the mean is returned. (Given as c(lower, upper)) |
Details
Implements the theory that since the read counts from each genetic element come from a (overdispersed) Poisson distribution with rate parameter lambda (=mean), this lambda can be inferred by simply taking the mean of the observations from that genetic element. A confidence interval is then constructed around the mean by random resampling with replacement. For each replicate and genetic element, the same number of samples is taken as there are read count observations associated with that particular genetic element. The observations of means are then sorted and the given lower and upper quantiles are returned.
Value
An object of class CNOGpro, with proposed copy number (floating point)
and the associated confidence interval for each genetic element in the table
of genes.
Author(s)
Ola Brynildsrud
Examples
1 2 3 4 | data(carsonella)
carsonella_normalized <- normalizeGC(carsonella)
carsonella_bootstrapped <- runBootstrap(carsonella, replicates=500)
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 0.9738434 0.89239711
2 CDS CRDC_00010 1 1332 2840 1509 1.0299858 0.97690330
3 CDS CRDC_00015 1 2806 3498 693 0.9621360 0.88976294
4 IG 1 3499 3499 1 0.8046182 0.01490034
5 CDS CRDC_00020 1 3500 3730 231 0.9126456 0.83069375
6 IG 1 3731 3735 5 1.0281232 0.03687833
7 CDS CRDC_00030 1 3736 4191 456 0.9536215 0.83441884
8 CDS CRDC_00035 1 4184 4366 183 1.0877246 1.04302354
9 IG 1 4367 4367 1 1.1324256 0.02980067
10 CDS CRDC_00040 1 4368 5813 1446 0.9638655 0.88843255
11 CDS CRDC_00045 1 5810 6562 753 0.9405837 0.86696676
12 CDS CRDC_00050 1 6559 7902 1344 0.9675285 0.90395374
13 CDS CRDC_00055 1 7899 8141 243 1.0765493 0.94244627
14 CDS CRDC_00060 1 8128 9015 888 0.9104106 0.83590887
15 IG 1 9016 9259 244 1.0579239 0.90892052
16 CDS CRDC_00070 -1 9260 9703 444 0.9784554 0.89650357
17 CDS CRDC_00075 -1 9679 11586 1908 0.8888051 0.83739890
18 CDS CRDC_00080 1 11564 13222 1659 0.9652107 0.90600253
19 CDS CRDC_00085 1 13203 13922 720 1.0318483 0.97597203
20 CDS CRDC_00090 -1 13910 14062 153 1.0430235 0.90892052
21 IG 1 14063 14190 128 1.2069272 1.17712657
22 tRNA CRDC_t01077 1 14191 14264 74 1.0579239 0.87911984
23 CDS CRDC_00095 -1 14252 15301 1050 1.0256398 0.94551947
24 CDS CRDC_00100 -1 15301 16245 945 0.9506415 0.86421951
25 CDS CRDC_00105 -1 16242 16943 702 0.9908724 0.92186518
26 CDS CRDC_00110 1 16923 17576 654 0.9600074 0.88337708
27 CDS CRDC_00115 1 17570 18196 627 0.9259495 0.83867607
28 CDS CRDC_00120 1 18171 18716 546 1.2090559 0.97458843
29 CDS CRDC_00125 1 18709 22044 3336 2.0509875 1.95653468
30 CDS CRDC_00130 1 22041 22526 486 0.9312710 0.84435239
31 IG 1 22527 22562 36 0.8344188 0.02980067
32 CDS CRDC_00135 1 22563 24635 2073 0.9089205 0.85267175
33 CDS CRDC_00140 -1 24632 24949 318 0.9945975 0.90147035
34 CDS CRDC_00145 1 24948 25139 192 0.8791198 0.80461816
35 CDS CRDC_00150 1 25114 25554 441 0.7450168 0.60182459
36 CDS CRDC_00155 1 25551 26567 1017 0.9184025 0.82764596
37 CDS CRDC_00160 1 26557 28203 1647 1.0546127 0.99540455
38 CDS CRDC_00165 1 28196 29179 984 1.0389598 0.95362153
39 IG 1 29180 29186 7 1.2516283 0.04470101
40 CDS CRDC_00170 1 29187 30392 1206 1.1095020 1.05098949
41 CDS CRDC_00175 -1 30379 30939 561 0.9408498 0.90993161
42 CDS CRDC_00180 1 30932 31075 144 0.8716697 0.80461816
43 CDS CRDC_00185 1 31072 32277 1206 0.8676580 0.79135113
44 CDS CRDC_00190 1 32274 33623 1350 0.9764687 0.90839901
45 CDS CRDC_00195 1 33620 34285 666 0.9621360 0.85346998
46 CDS CRDC_00200 1 34276 35097 822 1.0314344 0.89402018
47 IG 1 35098 35099 2 0.6854155 0.02980067
48 CDS CRDC_00205 1 35100 36245 1146 1.0132229 0.93986737
49 CDS CRDC_00210 -1 36207 37085 879 0.9503103 0.90229815
50 IG 1 37086 37086 1 0.9238209 0.02980067
51 CDS CRDC_00215 -1 37087 37302 216 0.9983225 0.92382085
52 IG 1 37303 37319 17 1.2069272 0.04470101
53 tRNA CRDC_t01079 1 37320 37390 71 1.2069272 0.03687833
54 tRNA CRDC_t01081 1 37391 37462 72 1.1920269 1.17712657
55 tRNA CRDC_t01083 1 37463 37551 89 1.2516283 1.17712657
56 CDS CRDC_00220 -1 37543 37839 297 1.0281232 0.90892052
57 CDS CRDC_00225 -1 37836 39131 1296 1.0526023 0.99350653
58 CDS CRDC_00230 1 39120 40364 1245 0.9547677 0.87562400
59 CDS CRDC_00235 1 40361 40882 522 1.0380568 0.94853058
60 CDS CRDC_00240 1 40879 41745 867 0.9536215 0.87464974
61 CDS CRDC_00245 1 41742 42482 741 0.9089205 0.78040512
62 IG 1 42483 42484 2 0.7301165 0.02980067
63 tRNA CRDC_t01085 1 42485 42557 73 0.8418690 0.73011648
64 tRNA CRDC_t01087 -1 42558 42630 73 1.0206730 0.95362153
65 IG 1 42631 42659 29 1.0877246 0.05960135
66 CDS CRDC_00255 -1 42660 43106 447 1.1200086 0.97845542
67 CDS CRDC_00260 -1 43096 44019 924 0.9292392 0.84390087
68 CDS CRDC_00265 1 44020 44712 693 1.0169480 0.94333098
69 CDS CRDC_00270 -1 44702 45778 1077 0.9414303 0.86686093
70 CDS CRDC_00275 -1 45765 47120 1356 0.9337544 0.87017964
71 CDS CRDC_00280 -1 47104 47301 198 1.0529571 0.98342220
72 CDS CRDC_00285 1 47291 47836 546 1.0494094 1.00784811
73 CDS CRDC_00290 1 47817 49058 1242 1.0304156 0.96393714
74 CDS CRDC_00295 1 49055 49351 297 1.0467486 0.93872119
75 CDS CRDC_00300 1 49348 49728 381 0.9804421 0.91786072
76 IG 1 49729 49872 144 0.9238209 0.89402018
77 CDS CRDC_00305 1 49873 50445 573 1.0877246 0.98970163
78 CDS CRDC_00310 1 50426 51178 753 0.9685219 0.89402018
79 CDS CRDC_00315 1 51175 52401 1227 0.9461714 0.88651680
80 CDS CRDC_00320 1 52388 53512 1125 0.9948840 0.94215973
81 CDS CRDC_00325 -1 53509 55101 1593 0.9667689 0.91242648
82 IG 1 55102 55107 6 1.0728242 0.04470101
83 CDS CRDC_00330 -1 55108 55392 285 1.0380568 0.99832254
84 IG 1 55393 55523 131 1.1075917 1.04302354
85 tRNA CRDC_t01089 1 55524 55596 73 1.2069272 0.03687833
86 IG 1 55597 55601 5 1.0579239 0.90892052
87 tRNA CRDC_t01091 1 55602 55675 74 0.9089205 0.03687833
88 IG 1 55676 55798 123 0.7599172 0.61091379
89 CDS CRDC_00340 1 55799 56260 462 0.8691863 0.73992587
90 CDS CRDC_00345 1 56260 56724 465 0.9511381 0.84186900
91 CDS CRDC_00350 1 56717 57868 1152 1.0368151 0.94787869
92 CDS CRDC_00355 1 57840 58379 540 0.9685219 0.90643713
93 CDS CRDC_00360 1 58357 58485 129 0.9238209 0.89402018
94 CDS CRDC_00365 1 58482 59249 768 0.8824310 0.83276324
95 CDS CRDC_00370 1 59246 60316 1071 0.9486547 0.88160323
96 IG 1 60317 60320 4 0.8791198 0.01490034
97 tRNA CRDC_t01093 1 60321 60392 72 0.8791198 0.02980067
98 CDS CRDC_00375 -1 60384 61319 936 0.9915497 0.90214764
99 CDS CRDC_00380 -1 61316 62047 732 1.0579239 0.98155966
100 CDS CRDC_00385 -1 62044 62721 678 1.0523363 1.00018508
101 CDS CRDC_00390 -1 62718 63320 603 0.8684767 0.78971783
102 CDS CRDC_00395 -1 63317 63859 543 0.9908724 0.90892052
103 IG 1 63860 63866 7 0.9387212 0.03687833
104 tRNA CRDC_t01095 1 63867 63939 73 0.9312710 0.92382085
105 tRNA CRDC_t01097 1 63940 64010 71 1.0579239 0.92382085
106 IG 1 64011 64012 2 1.1920269 0.03687833
107 tRNA CRDC_t01099 1 64013 64084 72 1.1920269 0.02980067
108 IG 1 64085 64250 166 0.9188541 0.64071446
109 CDS CRDC_00400 -1 64251 64583 333 0.8381439 0.70031581
110 CDS CRDC_00405 1 64584 65036 453 0.9263042 0.84931917
111 IG 1 65037 65097 61 0.7748175 0.02980067
112 CDS CRDC_00415 1 65098 66903 1806 0.9774621 0.91935075
113 IG 1 66904 66953 50 0.9238209 0.02980067
114 CDS CRDC_00420 1 66954 67652 699 0.9349961 0.88098239
115 CDS CRDC_00425 1 67646 68098 453 0.8493192 0.78375769
116 CDS CRDC_00430 1 68091 68642 552 0.9876794 0.90029961
117 CDS CRDC_00435 1 68632 71529 2898 1.0385534 0.99503204
118 IG 1 71530 71533 4 0.8940202 0.02980067
119 tRNA CRDC_t01101 1 71534 71614 81 0.9014703 0.89402018
120 IG 1 71615 71622 8 0.9089205 0.02980067
121 CDS CRDC_00440 1 71623 73176 1554 1.0560613 0.97131568
122 CDS CRDC_00445 1 73163 73357 195 0.8244853 0.71521614
123 CDS CRDC_00450 1 73354 74283 930 0.9789521 0.93574112
124 CDS CRDC_00455 1 74276 75442 1167 0.9582062 0.90083995
125 IG 1 75443 75448 6 0.9834222 0.02980067
126 tRNA CRDC_t01103 1 75449 75522 74 0.9834222 0.98342220
127 tRNA CRDC_t01105 1 75523 75595 73 0.9834222 0.02980067
128 IG 1 75596 75597 2 0.9834222 0.04470101
129 tRNA CRDC_t01107 1 75598 75673 76 1.0355734 0.98342220
130 IG 1 75674 75693 20 1.0877246 0.02980067
131 CDS CRDC_00460 1 75694 76272 579 1.0153515 0.93233533
132 CDS CRDC_00465 1 76253 77326 1074 0.9995642 0.94551947
133 CDS CRDC_00470 1 77326 78420 1095 0.9660385 0.88715982
134 CDS CRDC_00475 1 78417 79682 1266 0.9295518 0.87109659
135 CDS CRDC_00480 1 79669 79878 210 0.7946846 0.65561480
136 IG 1 79879 79924 46 0.9834222 0.92382085
137 tRNA CRDC_t01109 1 79925 80009 85 0.9536215 0.86421951
138 IG 1 80010 80074 65 0.8642195 0.02980067
139 CDS CRDC_00485 1 80075 80572 498 1.0554405 0.89402018
140 CDS CRDC_00490 -1 80573 83617 3045 1.0225356 0.96619369
141 IG 1 83618 83625 8 1.0877246 0.02980067
142 CDS CRDC_00495 1 83626 84984 1359 1.0483451 0.96740434
143 CDS CRDC_00500 1 84977 86014 1038 0.8853283 0.83128356
144 CDS CRDC_00505 1 86007 87371 1365 0.9791650 0.92539071
145 CDS CRDC_00510 1 87355 87909 555 1.0025798 0.87464974
146 CDS CRDC_00515 1 87902 88948 1047 0.9739402 0.87641069
147 CDS CRDC_00520 1 88941 89969 1029 1.0470873 0.94613749
148 CDS CRDC_00525 1 89966 90523 558 0.9536215 0.84506193
149 IG 1 90524 90526 3 0.7003158 0.02980067
150 CDS CRDC_00530 1 90527 91540 1014 0.9766493 0.89595045
151 tRNA CRDC_t01111 1 91520 91598 79 0.7897178 0.02980067
152 IG 1 91599 91608 10 0.8940202 0.78971783
153 CDS CRDC_00535 1 91609 92349 741 0.9163707 0.85765405
154 CDS CRDC_00540 1 92339 92710 372 0.8850800 0.82249857
155 CDS CRDC_00545 -1 92698 93027 330 0.9625617 0.91190058
156 CDS CRDC_00550 -1 93020 93562 543 0.9511381 0.87284929
157 CDS CRDC_00555 -1 93549 94112 564 0.9153064 0.63198712
158 CDS CRDC_00560 -1 94109 95335 1227 0.1272259 0.00000000
159 IG 1 95336 95409 74 1.2665286 1.22182758
160 CDS CRDC_00565 1 95410 95619 210 1.1522927 1.04302354
161 IG 1 95620 95989 370 0.9871473 0.81206833
162 CDS CRDC_00570 -1 95990 96304 315 0.9089205 0.75380802
163 CDS CRDC_00575 -1 96288 96482 195 0.9039537 0.68541547
164 CDS CRDC_00580 -1 96430 96960 531 0.9014703 0.80201060
165 CDS CRDC_00585 -1 96960 97568 609 0.9557501 0.85996227
166 IG 1 97569 97602 34 0.9312710 0.80461816
167 CDS CRDC_00590 -1 97603 98067 465 1.0370634 0.89998032
168 CDS CRDC_00595 -1 98048 99706 1659 0.9834222 0.92713204
169 CDS CRDC_00600 -1 99690 100616 927 1.0470873 0.96303583
170 CDS CRDC_00605 -1 100604 100729 126 0.9759720 0.92382085
171 CDS CRDC_00610 1 100728 101990 1263 1.0201000 0.97135866
172 CDS CRDC_00615 1 101980 102255 276 1.1100751 1.03184829
173 CDS CRDC_00620 1 102242 103780 1539 0.9824909 0.94710263
174 IG 1 103781 103901 121 0.9387212 0.90892052
175 CDS CRDC_00630 1 103902 104132 231 1.0032893 0.90892052
176 CDS CRDC_00635 -1 104116 104940 825 1.0662018 0.96843908
177 CDS CRDC_00640 -1 104933 105976 1044 0.9766493 0.87705412
178 CDS CRDC_00645 -1 105963 106940 978 0.9414303 0.89943849
179 IG 1 106941 106942 2 1.0728242 0.05177867
180 tRNA CRDC_t01113 -1 106943 107015 73 1.0355734 0.99832254
181 IG 1 107016 107107 92 0.9461714 0.89402018
182 CDS CRDC_00650 1 107108 108400 1293 0.8917278 0.83098030
183 CDS CRDC_00655 1 108390 108575 186 1.0082561 0.86421951
184 CDS CRDC_00660 -1 108568 109743 1176 0.9765451 0.91115557
185 IG 1 109744 109778 35 1.0132229 0.02980067
186 tRNA CRDC_t01115 1 109779 109849 71 0.9461714 0.87911984
187 IG 1 109850 109852 3 0.8791198 0.02980067
188 tRNA CRDC_t01117 1 109853 109933 81 0.9312710 0.87911984
189 CDS CRDC_00665 -1 109915 110691 777 1.0579239 0.98616945
190 IG 1 110692 110709 18 1.0281232 0.95362153
191 tRNA CRDC_t01119 -1 110710 110783 74 0.9536215 0.02980067
192 CDS CRDC_00670 -1 110761 111081 321 1.0355734 0.91637069
193 CDS CRDC_00675 1 111075 112472 1398 0.9695152 0.89548538
194 tRNA CRDC_t01121 -1 112438 112510 73 1.1920269 1.14732590
195 IG 1 112511 112515 5 1.2367279 0.05960135
196 tRNA CRDC_t01123 -1 112516 112597 82 1.2367279 0.04470101
197 CDS CRDC_00680 -1 112575 113822 1248 1.0206730 0.95681446
198 CDS CRDC_00685 -1 113819 114811 993 0.9915497 0.90072533
199 CDS CRDC_00690 -1 114804 115706 903 1.0102428 0.90743048
200 CDS CRDC_00695 1 115671 117545 1875 0.9104106 0.83700777
201 CDS CRDC_00700 1 117517 118044 528 1.1349090 1.05047371
202 CDS CRDC_00705 -1 118037 118936 900 0.9640518 0.85747711
203 CDS CRDC_00710 -1 118933 119664 732 1.0039102 0.90608014
204 CDS CRDC_00715 -1 119661 120800 1140 1.0628907 0.96976356
205 IG 1 120801 120807 7 0.9089205 0.02980067
206 rRNA CRDC_r01133 -1 120808 120915 108 0.9461714 0.90892052
207 IG 1 120916 120936 21 0.9834222 0.04470101
208 rRNA CRDC_r01135 -1 120937 123723 2787 1.0836141 1.03631839
209 IG 1 123724 123770 47 1.0281232 0.02980067
210 rRNA CRDC_r01137 -1 123771 125293 1523 1.0551301 0.99969616
211 IG 1 125294 125369 76 1.0877246 0.96852186
212 CDS CRDC_00720 -1 125370 126251 882 1.0385534 0.95879939
213 CDS CRDC_00725 -1 126248 126394 147 0.9610717 0.89402018
214 CDS CRDC_00730 -1 126382 126570 189 0.9834222 0.92878763
215 IG 1 126571 126576 6 0.8791198 0.02980067
216 CDS CRDC_00735 -1 126577 126924 348 0.9983225 0.91488065
217 CDS CRDC_00740 -1 126921 128063 1143 0.9672802 0.89402018
218 CDS CRDC_00745 -1 128060 128869 810 1.0794466 1.01069809
219 CDS CRDC_00750 -1 128862 130169 1308 0.9227565 0.85985584
220 CDS CRDC_00755 -1 130169 131296 1128 1.1498093 1.05910349
221 CDS CRDC_00760 -1 131293 131487 195 1.0479903 0.95362153
222 CDS CRDC_00765 -1 131474 131671 198 0.8890534 0.70031581
223 CDS CRDC_00770 -1 131668 131895 228 1.0082561 0.92382085
224 IG 1 131896 131945 50 1.1398757 1.08772455
225 tRNA CRDC_t01125 1 131946 132018 73 1.1026249 1.01322287
226 IG 1 132019 132022 4 1.0132229 0.02980067
227 CDS CRDC_00775 -1 132023 133018 996 1.0863700 1.03147578
228 CDS CRDC_00780 -1 133019 133471 453 0.9387212 0.78658876
229 CDS CRDC_00785 -1 133392 135068 1677 0.9486547 0.87289068
230 CDS CRDC_00790 -1 135065 135670 606 0.9834222 0.87273399
231 CDS CRDC_00795 -1 135663 135800 138 0.8791198 0.70031581
232 CDS CRDC_00800 -1 135793 135930 138 0.7897178 0.70031581
233 CDS CRDC_00805 -1 135923 138373 2451 1.0048787 0.93332727
234 CDS CRDC_00810 -1 138370 138522 153 1.0529571 0.95362153
235 CDS CRDC_00815 -1 138507 139283 777 0.9834222 0.82962279
236 CDS CRDC_00820 -1 139270 139527 258 0.8791198 0.69659072
237 IG 1 139528 139531 4 0.8940202 0.02980067
238 CDS CRDC_00825 -1 139532 139831 300 0.8493192 0.77481749
239 IG 1 139832 139839 8 0.8046182 0.02980067
240 CDS CRDC_00830 -1 139840 140085 246 0.8940202 0.80461816
241 CDS CRDC_00835 -1 140069 141031 963 0.9035022 0.83848256
242 CDS CRDC_00840 -1 141028 141609 582 1.0047084 0.93233533
243 CDS CRDC_00845 -1 141609 141968 360 1.0020476 0.86421951
244 CDS CRDC_00850 -1 141955 142311 357 0.8552793 0.73011648
245 CDS CRDC_00855 -1 142308 142421 114 0.8567693 0.78971783
246 CDS CRDC_00860 -1 142399 142656 258 0.8977453 0.81206833
247 CDS CRDC_00865 -1 142657 143073 417 1.0996448 1.04004348
248 CDS CRDC_00870 -1 143055 143291 237 1.0877246 1.02812321
249 CDS CRDC_00875 -1 143288 143791 504 0.9859056 0.89755901
250 CDS CRDC_00880 -1 143788 144153 366 1.0907046 1.00428267
251 IG 1 144154 144155 2 0.9685219 0.04470101
252 CDS CRDC_00885 -1 144156 144446 291 1.0541988 0.96107169
253 IG 1 144447 144448 2 1.2665286 0.02980067
254 CDS CRDC_00890 -1 144449 144943 495 1.1249754 1.01570626
255 CDS CRDC_00895 -1 144940 145308 369 0.9655418 0.85527931
256 CDS CRDC_00900 -1 145305 145547 243 0.8791198 0.80461816
257 CDS CRDC_00905 -1 145540 145947 408 1.0102428 0.90296038
258 IG 1 145948 145951 4 1.2367279 0.04470101
259 CDS CRDC_00910 -1 145952 146554 603 0.9898081 0.89077404
260 CDS CRDC_00915 -1 146539 146856 318 0.8381439 0.79716799
261 CDS CRDC_00920 -1 146846 147109 264 1.0243981 0.85676934
262 CDS CRDC_00925 -1 147106 147807 702 1.0877246 1.02253558
263 CDS CRDC_00930 -1 147804 148319 516 1.1820934 1.08027439
264 CDS CRDC_00935 -1 148316 148726 411 0.9893823 0.93872119
265 CDS CRDC_00940 -1 148723 149019 297 1.0243981 0.96852186
266 CDS CRDC_00945 -1 149016 150206 1191 1.0327079 0.94089893
267 IG 1 150207 150225 19 1.2218276 0.02980067
268 CDS CRDC_00950 -1 150226 152262 2037 1.0259946 0.97206956
269 CDS CRDC_00955 -1 152259 152729 471 0.8691863 0.80461816
270 CDS CRDC_00960 -1 152722 153087 366 0.9163707 0.86794459
271 IG 1 153088 153096 9 0.9685219 0.03687833
272 CDS CRDC_00965 -1 153097 156993 3897 0.9942249 0.93517305
273 CDS CRDC_00970 -1 156969 160769 3801 1.0204820 0.98207544
274 CDS CRDC_00975 -1 160766 161110 345 0.9834222 0.90437591
275 CDS CRDC_00980 -1 161091 161525 435 0.9585883 0.85676934
276 CDS CRDC_00985 -1 161522 162094 573 1.0231564 0.87663646
277 CDS CRDC_00990 -1 162087 162500 414 0.9417013 0.76587729
278 IG 1 162501 162519 19 0.8642195 0.04470101
279 tRNA CRDC_t01127 -1 162520 162590 71 0.8642195 0.04470101
280 IG 1 162591 162602 12 0.9312710 0.86421951
281 tRNA CRDC_t01129 -1 162603 162673 71 0.9983225 0.02980067
282 IG 1 162674 162674 1 0.9983225 0.02980067
283 tRNA CRDC_t01131 -1 162675 162755 81 0.8716697 0.74501682
284 IG 1 162756 162812 57 0.7897178 0.74501682
285 CDS CRDC_00995 -1 162813 163088 276 0.8940202 0.81951850
286 CDS CRDC_01000 -1 163055 163558 504 0.8369022 0.81703511
287 CDS CRDC_01005 -1 163551 165356 1806 0.9849907 0.92184068
288 CDS CRDC_01010 -1 165349 166113 765 0.9652107 0.89646218
289 CDS CRDC_01015 1 166090 166839 750 0.8956758 0.76653953
290 CDS CRDC_01020 1 166826 167755 930 0.8478291 0.73082425
291 CDS CRDC_01025 1 167743 167955 213 0.9486547 0.83441884
292 CDS CRDC_01030 1 167946 168410 465 1.0455069 0.97218486
293 CDS CRDC_01035 1 168403 169779 1377 1.0153515 0.93334643
294 CDS CRDC_01040 1 169776 170969 1194 0.9834222 0.93353473
295 CDS CRDC_01045 1 170962 171711 750 0.9072649 0.83938561
296 CDS CRDC_01050 1 171708 172331 624 1.0345091 0.95888986
297 IG 1 172332 172439 108 0.9014703 0.81951850
298 CDS CRDC_01060 1 172440 172988 549 1.0181897 0.96107169
299 IG 1 172989 173016 28 1.0430235 0.95362153
300 CDS CRDC_01065 -1 173017 173220 204 1.0430235 0.95362153
301 IG 1 173221 173286 66 1.0877246 0.02197800
302 CDS CRDC_01070 -1 173287 173964 678 0.9443088 0.77756474
303 IG 1 173965 174014 50 0.3650582 0.08940202
Upperbound
1 1.0531611
2 1.0835571
3 1.0366377
4 0.7897178
5 0.9983225
6 1.0132229
7 1.0460036
8 1.1324256
9 1.0877246
10 1.0453750
11 1.0188105
12 1.0276514
13 1.1771266
14 0.9775366
15 1.2069272
16 1.0628907
17 0.9439363
18 1.0281232
19 1.0933122
20 1.1771266
21 1.2367279
22 1.2367279
23 1.0977202
24 1.0461526
25 1.0682144
26 1.0569128
27 1.0174801
28 1.4900336
29 2.1287870
30 1.0206730
31 0.8195185
32 0.9726195
33 1.1063500
34 0.9387212
35 0.8612394
36 1.0193523
37 1.1117307
38 1.1242981
39 1.2218276
40 1.1719974
41 0.9706505
42 0.9387212
43 0.9479479
44 1.0544720
45 1.0803276
46 1.1597842
47 0.6705151
48 1.0699874
49 1.0148785
50 0.9089205
51 1.1361506
52 1.1920269
53 1.1920269
54 1.2069272
55 1.3261299
56 1.2292777
57 1.1196538
58 1.0413329
59 1.1287626
60 1.0385534
61 1.0226287
62 0.7152161
63 0.9536215
64 1.0877246
65 1.0579239
66 1.2342445
67 1.0118683
68 1.0765493
69 1.0403821
70 0.9978507
71 1.1026249
72 1.0919818
73 1.1095020
74 1.1645544
75 1.0430235
76 0.9536215
77 1.1707407
78 1.0504737
79 1.0153515
80 1.0585256
81 1.0185256
82 1.0579239
83 1.0728242
84 1.2069272
85 1.1771266
86 1.2069272
87 0.8940202
88 0.9089205
89 0.9747924
90 1.0355734
91 1.1243856
92 1.0306066
93 0.9536215
94 0.9320988
95 1.0163582
96 0.8642195
97 0.8642195
98 1.0687605
99 1.1473259
100 1.1119376
101 0.9526104
102 1.0592277
103 0.9238209
104 0.9387212
105 1.1920269
106 1.1771266
107 1.1473259
108 1.1920269
109 0.9759720
110 1.0008059
111 0.7748175
112 1.0367468
113 0.9089205
114 0.9759720
115 0.9178607
116 1.0643097
117 1.0820252
118 0.8791198
119 0.9089205
120 0.8940202
121 1.1450210
122 0.9536215
123 1.0281232
124 1.0097843
125 0.9685219
126 0.9834222
127 0.9685219
128 0.9685219
129 1.0877246
130 1.0728242
131 1.0909707
132 1.0474005
133 1.0610592
134 0.9954857
135 0.8840866
136 1.0430235
137 1.0430235
138 0.8493192
139 1.2441781
140 1.0689012
141 1.0806469
142 1.1228468
143 0.9418565
144 1.0286820
145 1.1112458
146 1.0877246
147 1.1527442
148 1.0675559
149 0.6854155
150 1.0775991
151 0.7748175
152 0.9983225
153 0.9796971
154 0.9686709
155 1.0132229
156 1.0355734
157 1.1143855
158 0.3427077
159 1.3112296
160 1.2171091
161 1.1622262
162 1.0670131
163 1.0728242
164 1.0095599
165 1.0356266
166 1.0579239
167 1.1565641
168 1.0438513
169 1.1446845
170 1.0281232
171 1.0706465
172 1.1622262
173 1.0244447
174 0.9834222
175 1.1771266
176 1.1630954
177 1.0986289
178 0.9807130
179 1.0579239
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287 1.0516501
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292 1.1200086
293 1.1026249
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298 1.0691612
299 1.1324256
300 1.0877246
301 1.0728242
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