#=GENOME_DIFF 1.0 #=CREATED 09:19:12 20 Jul 2021 #=PROGRAM breseq 0.35.7 revision b7a44cd89118 #=COMMAND /Users/jbarrick/Library/Developer/Xcode/DerivedData/breseq-canagyzpaxpsjgbtjxenmavcspzz/Build/Products/Debug/breseq --junction-only-reference pBTK622_tdk-kanR_cassette_for_Golden_Transformation.gbk -r Acinetobacter-baylyi-ADP1-WT.gff3 G2_CCGTCC_L007_R1_001.fastq.gz G2_CCGTCC_L007_R2_001.fastq.gz #=REFSEQ Acinetobacter-baylyi-ADP1-WT.gff3 #=REFSEQ pBTK622_tdk-kanR_cassette_for_Golden_Transformation.gbk #=READSEQ G2_CCGTCC_L007_R1_001.fastq.gz #=READSEQ G2_CCGTCC_L007_R2_001.fastq.gz #=CONVERTED-BASES 126730926 #=CONVERTED-READS 1005801 #=INPUT-BASES 126821016 #=INPUT-READS 1006516 #=MAPPED-BASES 123992720 #=MAPPED-READS 985191 DEL 1 6,13 ADP1-WT 321574 1237 DEL 2 7,14 ADP1-WT 941306 3549 mediated=IS1236 DEL 3 8,15 ADP1-WT 1248192 1237 DEL 4 10,18 ADP1-WT 1799601 1237 DEL 5 11,19 ADP1-WT 2726455 1268 MC 6 . ADP1-WT 321574 322810 0 0 left_inside_cov=0 left_outside_cov=44 right_inside_cov=0 right_outside_cov=44 MC 7 . ADP1-WT 941306 944854 0 0 left_inside_cov=0 left_outside_cov=39 right_inside_cov=0 right_outside_cov=39 MC 8 . ADP1-WT 1248192 1249428 0 0 left_inside_cov=0 left_outside_cov=36 right_inside_cov=0 right_outside_cov=37 MC 9 . ADP1-WT 1668723 1722720 0 0 left_inside_cov=0 left_outside_cov=40 right_inside_cov=0 right_outside_cov=36 MC 10 . ADP1-WT 1799601 1800837 0 0 left_inside_cov=0 left_outside_cov=47 right_inside_cov=0 right_outside_cov=47 MC 11 . ADP1-WT 2726455 2727722 0 0 left_inside_cov=0 left_outside_cov=30 right_inside_cov=0 right_outside_cov=30 JC 12 . ADP1-WT 1 1 ADP1-WT 3600835 -1 0 alignment_overlap=0 circular_chromosome=1 coverage_minus=14 coverage_plus=21 flanking_left=126 flanking_right=126 frequency=1 junction_possible_overlap_registers=125 key=ADP1-WT__1__1__ADP1-WT__3600835__-1__0____126__126__0__0 max_left=121 max_left_minus=113 max_left_plus=121 max_min_left=60 max_min_left_minus=31 max_min_left_plus=60 max_min_right=63 max_min_right_minus=62 max_min_right_plus=63 max_pos_hash_score=250 max_right=123 max_right_minus=117 max_right_plus=123 neg_log10_pos_hash_p_value=0.2 new_junction_coverage=1.04 new_junction_read_count=36 polymorphism_frequency=1.000e+00 pos_hash_score=30 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=125 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=125 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=35 JC 13 . ADP1-WT 321573 -1 ADP1-WT 322811 1 0 alignment_overlap=2 coverage_minus=23 coverage_plus=21 flanking_left=126 flanking_right=126 frequency=1 junction_possible_overlap_registers=123 key=ADP1-WT__321573__-1__ADP1-WT__322809__1__2____126__126__0__0 max_left=123 max_left_minus=118 max_left_plus=123 max_min_left=61 max_min_left_minus=61 max_min_left_plus=59 max_min_right=59 max_min_right_minus=59 max_min_right_plus=50 max_pos_hash_score=246 max_right=121 max_right_minus=109 max_right_plus=121 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.29 new_junction_read_count=44 polymorphism_frequency=1.000e+00 pos_hash_score=40 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=2 side_1_possible_overlap_registers=125 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=123 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=44 JC 14 . ADP1-WT 941305 -1 ADP1-WT 944855 1 0 alignment_overlap=1 coverage_minus=17 coverage_plus=21 flanking_left=126 flanking_right=126 frequency=1 junction_possible_overlap_registers=124 key=ADP1-WT__941305__-1__ADP1-WT__944854__1__1____126__126__0__0 max_left=124 max_left_minus=124 max_left_plus=118 max_min_left=49 max_min_left_minus=33 max_min_left_plus=49 max_min_right=58 max_min_right_minus=56 max_min_right_plus=58 max_pos_hash_score=248 max_right=120 max_right_minus=114 max_right_plus=120 neg_log10_pos_hash_p_value=0.2 new_junction_coverage=1.10 new_junction_read_count=38 polymorphism_frequency=1.000e+00 pos_hash_score=31 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=1 side_1_possible_overlap_registers=125 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=124 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=38 JC 15 . ADP1-WT 1248191 -1 ADP1-WT 1249429 1 0 alignment_overlap=0 coverage_minus=13 coverage_plus=23 flanking_left=126 flanking_right=126 frequency=1 junction_possible_overlap_registers=125 key=ADP1-WT__1248191__-1__ADP1-WT__1249429__1__0____126__126__0__0 max_left=123 max_left_minus=123 max_left_plus=120 max_min_left=61 max_min_left_minus=58 max_min_left_plus=61 max_min_right=62 max_min_right_minus=60 max_min_right_plus=62 max_pos_hash_score=250 max_right=116 max_right_minus=110 max_right_plus=116 neg_log10_pos_hash_p_value=0.2 new_junction_coverage=1.04 new_junction_read_count=36 polymorphism_frequency=1.000e+00 pos_hash_score=32 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=125 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=125 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=36 JC 16 . ADP1-WT 1668722 -1 pYTK001_with_tdk_kan 14 1 0 alignment_overlap=0 coverage_minus=17 coverage_plus=23 flanking_left=126 flanking_right=126 frequency=1 junction_possible_overlap_registers=125 key=ADP1-WT__1668722__-1__pYTK001_with_tdk_kan__14__1__0____126__126__0__0 max_left=118 max_left_minus=118 max_left_plus=117 max_min_left=60 max_min_left_minus=60 max_min_left_plus=52 max_min_right=61 max_min_right_minus=49 max_min_right_plus=61 max_pos_hash_score=250 max_right=122 max_right_minus=122 max_right_plus=113 neg_log10_pos_hash_p_value=0.1 new_junction_coverage=2.30 new_junction_read_count=40 polymorphism_frequency=1.000e+00 pos_hash_score=37 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=125 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=125 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=40 JC 17 . ADP1-WT 1722721 1 pYTK001_with_tdk_kan 1688 -1 0 alignment_overlap=0 coverage_minus=18 coverage_plus=18 flanking_left=126 flanking_right=126 frequency=1 junction_possible_overlap_registers=125 key=ADP1-WT__1722721__1__pYTK001_with_tdk_kan__1688__-1__0____126__126__0__0 max_left=118 max_left_minus=118 max_left_plus=114 max_min_left=60 max_min_left_minus=60 max_min_left_plus=60 max_min_right=63 max_min_right_minus=63 max_min_right_plus=40 max_pos_hash_score=250 max_right=116 max_right_minus=90 max_right_plus=116 neg_log10_pos_hash_p_value=0.2 new_junction_coverage=2.07 new_junction_read_count=36 polymorphism_frequency=1.000e+00 pos_hash_score=30 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=125 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=125 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=36 JC 18 . ADP1-WT 1799600 -1 ADP1-WT 1800838 1 0 alignment_overlap=0 coverage_minus=28 coverage_plus=17 flanking_left=126 flanking_right=126 frequency=1 junction_possible_overlap_registers=125 key=ADP1-WT__1799600__-1__ADP1-WT__1800838__1__0____126__126__0__0 max_left=125 max_left_minus=125 max_left_plus=104 max_min_left=58 max_min_left_minus=55 max_min_left_plus=58 max_min_right=61 max_min_right_minus=61 max_min_right_plus=61 max_pos_hash_score=250 max_right=125 max_right_minus=116 max_right_plus=125 neg_log10_pos_hash_p_value=0.1 new_junction_coverage=1.35 new_junction_read_count=47 polymorphism_frequency=1.000e+00 pos_hash_score=35 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=125 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=125 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=45 JC 19 . ADP1-WT 2726454 -1 ADP1-WT 2727723 1 0 alignment_overlap=0 coverage_minus=13 coverage_plus=17 flanking_left=126 flanking_right=126 frequency=1 junction_possible_overlap_registers=125 key=ADP1-WT__2726454__-1__ADP1-WT__2727723__1__0____126__126__0__0 max_left=121 max_left_minus=121 max_left_plus=119 max_min_left=60 max_min_left_minus=60 max_min_left_plus=60 max_min_right=58 max_min_right_minus=38 max_min_right_plus=58 max_pos_hash_score=250 max_right=122 max_right_minus=108 max_right_plus=122 neg_log10_pos_hash_p_value=0.3 new_junction_coverage=0.86 new_junction_read_count=30 polymorphism_frequency=1.000e+00 pos_hash_score=28 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=125 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=125 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=30 UN 20 . ADP1-WT 18149 23676 UN 21 . ADP1-WT 212948 215271 UN 22 . ADP1-WT 215413 218478 UN 23 . ADP1-WT 297660 297725 UN 24 . ADP1-WT 321574 322810 UN 25 . ADP1-WT 645774 650339 UN 26 . ADP1-WT 650565 650565 UN 27 . ADP1-WT 650569 651048 UN 28 . ADP1-WT 651265 651388 UN 29 . ADP1-WT 651391 651391 UN 30 . ADP1-WT 868630 868730 UN 31 . ADP1-WT 919844 919844 UN 32 . ADP1-WT 919849 919849 UN 33 . ADP1-WT 919851 919888 UN 34 . ADP1-WT 941306 944854 UN 35 . ADP1-WT 1235471 1235525 UN 36 . ADP1-WT 1248192 1249428 UN 37 . ADP1-WT 1446536 1447236 UN 38 . ADP1-WT 1447534 1448030 UN 39 . ADP1-WT 1660764 1665964 UN 40 . ADP1-WT 1668723 1722720 UN 41 . ADP1-WT 1799601 1800837 UN 42 . ADP1-WT 1848838 1848839 UN 43 . ADP1-WT 1848847 1851169 UN 44 . ADP1-WT 1855869 1855869 UN 45 . ADP1-WT 1855878 1858204 UN 46 . ADP1-WT 2222817 2222874 UN 47 . ADP1-WT 2371896 2372038 UN 48 . ADP1-WT 2372194 2372194 UN 49 . ADP1-WT 2372196 2372197 UN 50 . ADP1-WT 2372199 2372199 UN 51 . ADP1-WT 2372201 2372201 UN 52 . ADP1-WT 2372203 2372203 UN 53 . ADP1-WT 2372205 2372205 UN 54 . ADP1-WT 2372207 2372207 UN 55 . ADP1-WT 2372209 2372209 UN 56 . ADP1-WT 2372211 2372315 UN 57 . ADP1-WT 2726455 2727722 UN 58 . ADP1-WT 2803645 2804803 UN 59 . ADP1-WT 2805662 2805662 UN 60 . ADP1-WT 2805837 2807042 UN 61 . ADP1-WT 2944261 2949787 UN 62 . ADP1-WT 3073136 3073136 UN 63 . ADP1-WT 3073138 3073139 UN 64 . ADP1-WT 3073142 3073142 UN 65 . ADP1-WT 3073148 3073148 UN 66 . ADP1-WT 3073150 3073150 UN 67 . ADP1-WT 3073152 3073152 UN 68 . ADP1-WT 3073155 3078945 UN 69 . ADP1-WT 3174558 3174649 UN 70 . ADP1-WT 3332283 3332402 UN 71 . ADP1-WT 3360679 3360694 UN 72 . ADP1-WT 3360696 3360697 UN 73 . ADP1-WT 3360699 3360700 UN 74 . ADP1-WT 3561578 3567069