Mercurial > repos > cpt > cpt_phageqc_annotations

comparison cpt_phageqc_annotation/test-data/PhageQC_Out.gff3 @ 0:c3140b08d703 draft default tip

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author cpt
date Fri, 17 Jun 2022 13:00:50 +0000
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-1:000000000000 0:c3140b08d703
1 ##gff-version 3
2 AY216660.2 feature gene 25 34 . + . note=Missing RBS;ID=CPT-T1_001.gene;Name=
3 AY216660.2 feature gene 574 583 . + . note=Missing RBS;ID=CPT-T1_002.gene;Name=
4 AY216660.2 feature gene 2215 2224 . + . note=Missing RBS;ID=CPT-T1_003.gene;Name=
5 AY216660.2 feature gene 3481 3490 . + . note=Missing RBS;ID=CPT-T1_004.gene;Name=
6 AY216660.2 feature gene 4249 4258 . + . note=Missing RBS;ID=CPT-T1_005.gene;Name=
7 AY216660.2 feature gene 5374 5383 . + . note=Missing RBS;ID=CPT-T1_006.gene;Name=
8 AY216660.2 feature gene 5911 5920 . + . note=Missing RBS;ID=CPT-T1_007.gene;Name=
9 AY216660.2 feature gene 6769 6778 . + . note=Missing RBS;ID=CPT-T1_008.gene;Name=
10 AY216660.2 feature gene 7779 7788 . + . note=Missing RBS;ID=CPT-T1_009.gene;Name=
11 AY216660.2 feature gene 8112 8121 . + . note=Missing RBS;ID=CPT-T1_010.gene;Name=
12 AY216660.2 feature gene 8519 8528 . + . note=Missing RBS;ID=CPT-T1_011.gene;Name=
13 AY216660.2 feature gene 8882 8891 . + . note=Missing RBS;ID=CPT-T1_012.gene;Name=
14 AY216660.2 feature gene 9317 9326 . + . note=Missing RBS;ID=CPT-T1_013.gene;Name=
15 AY216660.2 feature gene 9718 9727 . + . note=Missing RBS;ID=CPT-T1_014.gene;Name=
16 AY216660.2 feature gene 10501 10510 . + . note=Missing RBS;ID=CPT-T1_015.gene;Name=
17 AY216660.2 feature gene 10501 10510 . + . note=Missing RBS;ID=CPT-T1_016.gene;Name=
18 AY216660.2 feature gene 11177 11186 . + . note=Missing RBS;ID=CPT-T1_017.gene;Name=
19 AY216660.2 feature gene 14052 14061 . + . note=Missing RBS;ID=CPT-T1_018.gene;Name=
20 AY216660.2 feature gene 14485 14494 . + . note=Missing RBS;ID=CPT-T1_019.gene;Name=
21 AY216660.2 feature gene 15264 15273 . + . note=Missing RBS;ID=CPT-T1_020.gene;Name=
22 AY216660.2 feature gene 15994 16003 . + . note=Missing RBS;ID=CPT-T1_021.gene;Name=
23 AY216660.2 feature gene 16673 16682 . + . note=Missing RBS;ID=CPT-T1_022.gene;Name=
24 AY216660.2 feature gene 20236 20245 . + . note=Missing RBS;ID=CPT-T1_023.gene;Name=
25 AY216660.2 feature gene 20541 20550 . + . note=Missing RBS;ID=CPT-T1_024.gene;Name=
26 AY216660.2 feature gene 21524 21533 . - . note=Missing RBS;ID=CPT-T1_025.gene;Name=
27 AY216660.2 feature gene 21740 21749 . + . note=Missing RBS;ID=CPT-T1_026.gene;Name=
28 AY216660.2 feature gene 22005 22014 . + . note=Missing RBS;ID=CPT-T1_027.gene;Name=
29 AY216660.2 feature gene 23114 23123 . + . note=Missing RBS;ID=CPT-T1_028.gene;Name=
30 AY216660.2 feature gene 23839 23848 . + . note=Missing RBS;ID=CPT-T1_029.gene;Name=
31 AY216660.2 feature gene 26556 26565 . - . note=Missing RBS;ID=CPT-T1_030.gene;Name=
32 AY216660.2 feature gene 26606 26615 . - . note=Missing RBS;ID=CPT-T1_031.gene;Name=
33 AY216660.2 feature gene 27591 27600 . - . note=Missing RBS;ID=CPT-T1_032.gene;Name=
34 AY216660.2 feature gene 28104 28113 . - . note=Missing RBS;ID=CPT-T1_033.gene;Name=
35 AY216660.2 feature gene 28153 28162 . + . note=Missing RBS;ID=CPT-T1_034.gene;Name=
36 AY216660.2 feature gene 30166 30175 . + . note=Missing RBS;ID=CPT-T1_035.gene;Name=
37 AY216660.2 feature gene 30654 30663 . + . note=Missing RBS;ID=CPT-T1_036.gene;Name=
38 AY216660.2 feature gene 31362 31371 . + . note=Missing RBS;ID=CPT-T1_037.gene;Name=
39 AY216660.2 feature gene 31680 31689 . + . note=Missing RBS;ID=CPT-T1_038.gene;Name=
40 AY216660.2 feature gene 31866 31875 . + . note=Missing RBS;ID=CPT-T1_039.gene;Name=
41 AY216660.2 feature gene 32084 32093 . + . note=Missing RBS;ID=CPT-T1_040.gene;Name=
42 AY216660.2 feature gene 32452 32461 . + . note=Missing RBS;ID=CPT-T1_041.gene;Name=
43 AY216660.2 feature gene 33658 33667 . + . note=Missing RBS;ID=CPT-T1_042.gene;Name=
44 AY216660.2 feature gene 34211 34220 . + . note=Missing RBS;ID=CPT-T1_043.gene;Name=
45 AY216660.2 feature gene 34510 34519 . + . note=Missing RBS;ID=CPT-T1_044.gene;Name=
46 AY216660.2 feature gene 34724 34733 . + . note=Missing RBS;ID=CPT-T1_045.gene;Name=
47 AY216660.2 feature gene 35212 35221 . + . note=Missing RBS;ID=CPT-T1_046.gene;Name=
48 AY216660.2 feature gene 36185 36194 . - . note=Missing RBS;ID=CPT-T1_047.gene;Name=
49 AY216660.2 feature gene 37761 37770 . - . note=Missing RBS;ID=CPT-T1_048.gene;Name=
50 AY216660.2 feature gene 38300 38309 . - . note=Missing RBS;ID=CPT-T1_049.gene;Name=
51 AY216660.2 feature gene 38712 38721 . - . note=Missing RBS;ID=CPT-T1_050.gene;Name=
52 AY216660.2 feature gene 39000 39009 . - . note=Missing RBS;ID=CPT-T1_051.gene;Name=
53 AY216660.2 feature gene 39228 39237 . - . note=Missing RBS;ID=CPT-T1_052.gene;Name=
54 AY216660.2 feature gene 39450 39459 . - . note=Missing RBS;ID=CPT-T1_053.gene;Name=
55 AY216660.2 feature gene 39764 39773 . - . note=Missing RBS;ID=CPT-T1_054.gene;Name=
56 AY216660.2 feature gene 39984 39993 . - . note=Missing RBS;ID=CPT-T1_055.gene;Name=
57 AY216660.2 feature gene 40348 40357 . - . note=Missing RBS;ID=CPT-T1_056.gene;Name=
58 AY216660.2 feature gene 41005 41014 . + . note=Missing RBS;ID=CPT-T1_057.gene;Name=
59 AY216660.2 feature gene 41591 41600 . + . note=Missing RBS;ID=CPT-T1_058.gene;Name=
60 AY216660.2 feature gene 41998 42007 . + . note=Missing RBS;ID=CPT-T1_059.gene;Name=
61 AY216660.2 feature gene 42232 42241 . + . note=Missing RBS;ID=CPT-T1_060.gene;Name=
62 AY216660.2 feature gene 42458 42467 . + . note=Missing RBS;ID=CPT-T1_061.gene;Name=
63 AY216660.2 feature gene 42565 42574 . + . note=Missing RBS;ID=CPT-T1_062.gene;Name=
64 AY216660.2 feature gene 42809 42818 . + . note=Missing RBS;ID=CPT-T1_063.gene;Name=
65 AY216660.2 feature gene 43370 43379 . + . note=Missing RBS;ID=CPT-T1_064.gene;Name=
66 AY216660.2 feature gene 43855 43864 . + . note=Missing RBS;ID=CPT-T1_065.gene;Name=
67 AY216660.2 feature gene 44083 44092 . + . note=Missing RBS;ID=CPT-T1_066.gene;Name=
68 AY216660.2 feature gene 44512 44521 . + . note=Missing RBS;ID=CPT-T1_067.gene;Name=
69 AY216660.2 feature gene 44610 44619 . + . note=Missing RBS;ID=CPT-T1_068.gene;Name=
70 AY216660.2 feature gene 44883 44892 . + . note=Missing RBS;ID=CPT-T1_069.gene;Name=
71 AY216660.2 feature gene 45413 45422 . + . note=Missing RBS;ID=CPT-T1_070.gene;Name=
72 AY216660.2 feature gene 45926 45935 . + . note=Missing RBS;ID=CPT-T1_071.gene;Name=
73 AY216660.2 feature gene 46429 46438 . + . note=Missing RBS;ID=CPT-T1_072.gene;Name=
74 AY216660.2 feature gene 47070 47079 . + . note=Missing RBS;ID=CPT-T1_073.gene;Name=
75 AY216660.2 feature gene 47278 47287 . + . note=Missing RBS;ID=CPT-T1_074.gene;Name=
76 AY216660.2 feature gene 47622 47631 . + . note=Missing RBS;ID=CPT-T1_075.gene;Name=
77 AY216660.2 feature gene 47849 47858 . + . note=Missing RBS;ID=CPT-T1_076.gene;Name=
78 AY216660.2 feature gene 48220 48229 . + . note=Missing RBS;ID=CPT-T1_077.gene;Name=
79 AY216660.2 feature gene 48362 48371 . + . note=Missing RBS;ID=CPT-T1_078.gene;Name=
80 AY216660.2 feature gene 48549 48558 . + . note=Missing RBS;ID=CPT-T1_079.gene;Name=
81 AY216660.2 feature gene 2185 2238 . . . note=Excessive gap%2C 54 bases;
82 AY216660.2 feature gene 5877 5937 . . . note=Excessive gap%2C 61 bases;
83 AY216660.2 feature gene 6706 6795 . . . note=Excessive gap%2C 90 bases;
84 AY216660.2 feature gene 10415 10527 . . . note=Excessive gap%2C 113 bases;
85 AY216660.2 feature gene 14433 14511 . . . note=Excessive gap%2C 79 bases;
86 AY216660.2 feature gene 14424 14540 . + . note=Possible gene;
87 AY216660.2 feature Shine_Dalgarno_sequence 14424 14433 . + . Parent=<unknown id>;
88 AY216660.2 feature CDS 14439 14540 . + 0 Parent=<unknown id>;
89 AY216660.2 feature gene 14447 14451 . - . note=Possible gene;
90 AY216660.2 feature Shine_Dalgarno_sequence 14452 14461 . - . Parent=<unknown id>;
91 AY216660.2 feature CDS 14447 14524 . - 0 Parent=<unknown id>;
92 AY216660.2 feature gene 16622 16698 . . . note=Excessive gap%2C 77 bases;
93 AY216660.2 feature gene 21507 21765 . . . note=Excessive gap%2C 259 bases;
94 AY216660.2 feature gene 21907 22033 . . . note=Excessive gap%2C 127 bases;
95 AY216660.2 feature gene 24290 24350 . . . note=Excessive gap%2C 61 bases;
96 AY216660.2 feature gene 24286 24390 . + . note=Possible gene;
97 AY216660.2 feature Shine_Dalgarno_sequence 24286 24295 . + . Parent=<unknown id>;
98 AY216660.2 feature CDS 24301 24390 . + 0 Parent=<unknown id>;
99 AY216660.2 feature gene 27574 27634 . . . note=Excessive gap%2C 61 bases;
100 AY216660.2 feature gene 28088 28180 . . . note=Excessive gap%2C 93 bases;
101 AY216660.2 feature gene 30613 30679 . . . note=Excessive gap%2C 67 bases;
102 AY216660.2 feature gene 30629 30718 . + . note=Possible gene;
103 AY216660.2 feature Shine_Dalgarno_sequence 30629 30638 . + . Parent=<unknown id>;
104 AY216660.2 feature CDS 30644 30718 . + 0 Parent=<unknown id>;
105 AY216660.2 feature gene 31642 31707 . . . note=Excessive gap%2C 66 bases;
106 AY216660.2 feature gene 32400 32477 . . . note=Excessive gap%2C 78 bases;
107 AY216660.2 feature gene 32385 32492 . + . note=Possible gene;
108 AY216660.2 feature Shine_Dalgarno_sequence 32385 32394 . + . Parent=<unknown id>;
109 AY216660.2 feature CDS 32400 32492 . + 0 Parent=<unknown id>;
110 AY216660.2 feature gene 33612 33683 . . . note=Excessive gap%2C 72 bases;
111 AY216660.2 feature gene 34167 34238 . . . note=Excessive gap%2C 72 bases;
112 AY216660.2 feature gene 34416 34533 . . . note=Excessive gap%2C 118 bases;
113 AY216660.2 feature gene 35639 35760 . . . note=Excessive gap%2C 122 bases;
114 AY216660.2 feature gene 35674 35678 . - . note=Possible gene;
115 AY216660.2 feature Shine_Dalgarno_sequence 35679 35688 . - . Parent=<unknown id>;
116 AY216660.2 feature CDS 35674 35754 . - 0 Parent=<unknown id>;
117 AY216660.2 feature gene 35674 35678 . - . note=Possible gene;
118 AY216660.2 feature Shine_Dalgarno_sequence 35679 35688 . - . Parent=<unknown id>;
119 AY216660.2 feature CDS 35674 35766 . - 0 Parent=<unknown id>;
120 AY216660.2 feature gene 38694 38773 . . . note=Excessive gap%2C 80 bases;
121 AY216660.2 feature gene 38719 38814 . + . note=Possible gene;
122 AY216660.2 feature Shine_Dalgarno_sequence 38719 38728 . + . Parent=<unknown id>;
123 AY216660.2 feature CDS 38734 38814 . + 0 Parent=<unknown id>;
124 AY216660.2 feature gene 38725 38814 . + . note=Possible gene;
125 AY216660.2 feature Shine_Dalgarno_sequence 38725 38734 . + . Parent=<unknown id>;
126 AY216660.2 feature CDS 38740 38814 . + 0 Parent=<unknown id>;
127 AY216660.2 feature gene 39212 39288 . . . note=Excessive gap%2C 77 bases;
128 AY216660.2 feature gene 40331 41030 . . . note=Excessive gap%2C 700 bases;
129 AY216660.2 feature gene 40416 40420 . - . note=Possible gene;
130 AY216660.2 feature Shine_Dalgarno_sequence 40421 40430 . - . Parent=<unknown id>;
131 AY216660.2 feature CDS 40416 40496 . - 0 Parent=<unknown id>;
132 AY216660.2 feature gene 40416 40420 . - . note=Possible gene;
133 AY216660.2 feature Shine_Dalgarno_sequence 40421 40430 . - . Parent=<unknown id>;
134 AY216660.2 feature CDS 40416 40511 . - 0 Parent=<unknown id>;
135 AY216660.2 feature gene 40416 40420 . - . note=Possible gene;
136 AY216660.2 feature Shine_Dalgarno_sequence 40421 40430 . - . Parent=<unknown id>;
137 AY216660.2 feature CDS 40416 40541 . - 0 Parent=<unknown id>;
138 AY216660.2 feature gene 40416 40420 . - . note=Possible gene;
139 AY216660.2 feature Shine_Dalgarno_sequence 40421 40430 . - . Parent=<unknown id>;
140 AY216660.2 feature CDS 40416 40559 . - 0 Parent=<unknown id>;
141 AY216660.2 feature gene 40416 40420 . - . note=Possible gene;
142 AY216660.2 feature Shine_Dalgarno_sequence 40421 40430 . - . Parent=<unknown id>;
143 AY216660.2 feature CDS 40416 40595 . - 0 Parent=<unknown id>;
144 AY216660.2 feature gene 40416 40420 . - . note=Possible gene;
145 AY216660.2 feature Shine_Dalgarno_sequence 40421 40430 . - . Parent=<unknown id>;
146 AY216660.2 feature CDS 40416 40637 . - 0 Parent=<unknown id>;
147 AY216660.2 feature gene 40817 40921 . + . note=Possible gene;
148 AY216660.2 feature Shine_Dalgarno_sequence 40817 40826 . + . Parent=<unknown id>;
149 AY216660.2 feature CDS 40832 40921 . + 0 Parent=<unknown id>;
150 AY216660.2 feature gene 41946 42023 . . . note=Excessive gap%2C 78 bases;
151 AY216660.2 feature gene 42765 42835 . . . note=Excessive gap%2C 71 bases;
152 AY216660.2 feature gene 43325 43395 . . . note=Excessive gap%2C 71 bases;
153 AY216660.2 feature gene 44031 44110 . . . note=Excessive gap%2C 80 bases;
154 AY216660.2 feature gene 44486 44538 . . . note=Excessive gap%2C 53 bases;
155 AY216660.2 feature gene 44853 44909 . . . note=Excessive gap%2C 57 bases;
156 AY216660.2 feature gene 45357 45439 . . . note=Excessive gap%2C 83 bases;
157 AY216660.2 feature gene 45368 45372 . - . note=Possible gene;
158 AY216660.2 feature Shine_Dalgarno_sequence 45373 45382 . - . Parent=<unknown id>;
159 AY216660.2 feature CDS 45368 45445 . - 0 Parent=<unknown id>;
160 AY216660.2 feature gene 45368 45372 . - . note=Possible gene;
161 AY216660.2 feature Shine_Dalgarno_sequence 45373 45382 . - . Parent=<unknown id>;
162 AY216660.2 feature CDS 45368 45463 . - 0 Parent=<unknown id>;
163 AY216660.2 feature gene 45368 45372 . - . note=Possible gene;
164 AY216660.2 feature Shine_Dalgarno_sequence 45373 45382 . - . Parent=<unknown id>;
165 AY216660.2 feature CDS 45368 45466 . - 0 Parent=<unknown id>;
166 AY216660.2 feature gene 45368 45372 . - . note=Possible gene;
167 AY216660.2 feature Shine_Dalgarno_sequence 45373 45382 . - . Parent=<unknown id>;
168 AY216660.2 feature CDS 45368 45475 . - 0 Parent=<unknown id>;
169 AY216660.2 feature gene 45368 45372 . - . note=Possible gene;
170 AY216660.2 feature Shine_Dalgarno_sequence 45373 45382 . - . Parent=<unknown id>;
171 AY216660.2 feature CDS 45368 45478 . - 0 Parent=<unknown id>;
172 AY216660.2 feature gene 45368 45372 . - . note=Possible gene;
173 AY216660.2 feature Shine_Dalgarno_sequence 45373 45382 . - . Parent=<unknown id>;
174 AY216660.2 feature CDS 45368 45481 . - 0 Parent=<unknown id>;
175 AY216660.2 feature gene 47027 47098 . . . note=Excessive gap%2C 72 bases;
176 AY216660.2 feature gene 48083 48246 . . . note=Excessive gap%2C 164 bases;
177 AY216660.2 feature gene 48086 48090 . - . note=Possible gene;
178 AY216660.2 feature Shine_Dalgarno_sequence 48091 48100 . - . Parent=<unknown id>;
179 AY216660.2 feature CDS 48086 48169 . - 0 Parent=<unknown id>;
180 AY216660.2 feature gene 48160 48164 . - . note=Possible gene;
181 AY216660.2 feature Shine_Dalgarno_sequence 48165 48174 . - . Parent=<unknown id>;
182 AY216660.2 feature CDS 48160 48255 . - 0 Parent=<unknown id>;
183 AY216660.2 feature gene 10528 10844 . . . note=Excessive Overlap;ID=CPT-T1_015.gene;Name=
184 AY216660.2 feature gene 26447 26536 . . . note=Excessive Overlap;ID=CPT-T1_030.gene;Name=
185 AY216660.2 feature gene 32112 32166 . . . note=Excessive Overlap;ID=CPT-T1_039.gene;Name=