New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1391495	NA (NA)	33 (0.700)	24/296	1.1	100%	intergenic (+146/‑127)	insH1/ynaJ	IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
	?	CP009273	= 1972751	0 (0.000)					intergenic (‑297/‑483)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

AAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/1391349‑1391495 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAAAGACCCATTTCTATTTGTAA  <  CP009273/1972751‑1972604                                                                                                                                                                                                                                                                                                         AAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAACAGGCTGATTCAAGGCGTTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTT                                                                                                                                                    >  2:513838/1‑149   AACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAA                                                                                                                                                  <  2:98528/149‑1   AACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTGACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTAAGTCAACCGAGAAGAATTTCCCCCAATATTCTCAGCTTCCTTAA                                                                                                                                                  >  1:692638/1‑149                  CTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTTATTGAGTGTTTT                                                                                                                                   <  2:558125/149‑1                    tacATGGCGAAGAAACGGTCCACATAGGCTGATTCAAGGCATTTACGGGAGACAAAACCGGCTCAAACATGAAGACATGAAATGACTGAGTCAGCCGAGAACAATTTCCCCCCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGT                                                                                                                                 <  1:538370/146‑1                    TAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGT                                                                                                                                 <  2:75463/149‑1                       ATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTG                                                                                                                              <  1:563884/149‑1                        TGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCTCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGA                                                                                                                             <  1:585034/149‑1                         GGCAAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGAT                                                                                                                            <  1:95791/149‑1                           CGAAGAAACGGTCTAGATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTTTGATCT                                                                                                                          <  1:133860/149‑1                           CGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCT                                                                                                                          >  2:1067/1‑149                                         AAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTAT                                                                                                            <  1:532567/149‑1                                           ATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTG                                                                                                          <  2:719489/149‑1                                            TAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGA                                                                                                         <  2:676149/149‑1                                            TAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGA                                                                                                         <  2:168867/149‑1                                              GGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGTGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAA                                                                                                       <  2:524071/149‑1                                                     TCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAG                                                                                                >  1:248547/1‑149                                                                 CGGGAGAAAAAATCGTCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTT                                                                                    <  2:30641/149‑1                                                                                GCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGATTTTCCCCGCTTATTCGCACCTTCCTTTAGTAAATGTTTTTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGT                                                                     <  1:702908/149‑1                                                                                                ATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGAAAGTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCG                                                     >  1:389556/1‑149                                                                                                             GTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAA                                        <  2:248547/149‑1                                                                                                                AGCTGAAAAGAATGTCCCCGTTTATTCGAACCTTCGTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCTCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAAT                                     <  1:483765/149‑1                                                                                                                      GAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCGTCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGA                               >  1:608629/1‑149                                                                                                                           atcTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGT                          <  2:593670/146‑1                                                                                                                           ATTTCCCCGCTTATTCGGACCGTCCTTAAGTAATTGAGAGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGGGCGTGTAGTGACGAGTACAGTTGCGAAAAAATAAAAAAAATCTTAGATAAGT                          <  1:235537/149‑1                                                                                                                           ATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATTTGGATGATGCATTATTGAAAATCGCAGCCCCCATCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGAGAAAAAAAAAAAAAAATCTTAGATAAGT                          <  1:1067/149‑1                                                                                                                                CCCGCTTATTCGCACCTTCTTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAAA                     <  1:621755/149‑1                                                                                                                                         taGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAACCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAAAGACCCATTT            <  1:668649/147‑1                                                                                                                                         TCGCTCCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATCATTGAATATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGAGTCGATTTAGCAAAAATCTTAGATAAGTGTAAAGACCCATTT            <  1:513838/149‑1                                                                                                                                              CCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCAGCTCCGTTGTATGTGCGTGCAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAAAGACCCATTTCTATT       <  2:373828/149‑1                                                                                                                                                  CCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCGCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTGAGATAAGTGTAAAGACCCATTTCTATTTGTA   >  2:519918/1‑149                                                                                                                                                   CTTAATTAATTGAGTGTTTTGTGTGCTCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGTGGGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGGAAAGACCCATTTCTATTTGTAA  <  1:44230/149‑1                                                                                                                                                   CTTAAGTAATTGAGTGTTTTGTGTGATCCGCATCACGGATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAAAGACCCATTTCTATTTGTAA  <  1:663866/149‑1                                                                                                                                                                                                                                                                                                         AAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/1391349‑1391495 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAAAGACCCATTTCTATTTGTAA  <  CP009273/1972751‑1972604

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.