New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1391495	NA (NA)	50 (0.920)	41/296	0.3	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

AACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/1391351‑1391495 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAAAGAC  <  CP009273/1972751‑1972620                                                                                                                                                                                                                                                                                       AACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAA                                                                                                                                  <  2:479399/149‑1   cgggggagagtGCCGTAAATGGGGAAGGAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTGCCCCGCTTATTCGCACCTTCCTTAAta                                                                                                                                <  1:303633/138‑3   CTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGT                                                                                                                                <  2:813807/149‑1    tgggttaAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCACTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTA                                                                                                                               <  1:520639/142‑1    TGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTA                                                                                                                               >  1:743764/1‑149       GGATAACGCCTTAAATGGTGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATT                                                                                                                            <  2:115911/149‑1        GATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTG                                                                                                                           <  2:411465/149‑1         ATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCTCTTATTCGCACCTTCCTTAAGTAATTGA                                                                                                                          <  2:582460/149‑1             CGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAGGTAATTGAGTGT                                                                                                                      >  2:419032/1‑149                  TAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGT                                                                                                                 <  2:431106/149‑1                  TAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGT                                                                                                                 >  2:67339/1‑149                        gaGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAACAATCAGCTCAAACATGAAGAAGTGAAATGACTGAGTCAGCCGGGAAGAATTTCCCCGCTTATTCGCACGTTCCTGAAGTAATTGCGGGTTTTGTGTGAac                                                                                                           >  1:387029/3‑147                         CGAAGAAAGGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCT                                                                                                          <  2:622168/149‑1                         CGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGCGATCT                                                                                                          <  1:561665/149‑1                                ACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATTAAGAAGTGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCAC                                                                                                   >  2:599045/1‑149                                    TCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCAT                                                                                               <  1:323695/149‑1                                      gAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAGATCGGCTCAAACCTGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCACACCTTCCTTAAGTAGCTGAGTGTTTTGTGTGATCTGCATCCCGCATTc                                                                                             >  1:157088/2‑148                                         ATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGTTCTGCATCACGCATTATTG                                                                                          >  1:779700/1‑149                                          TAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGA                                                                                         >  2:327966/1‑149                                             GCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAGGTAATTGGGTGTTTTTTGTGGTCTGCATAACACATTATTagaaa                                                                                      >  2:287747/1‑144                                                GATTCAAGGCATTTACGGGAGAAAAAATAGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCG                                                                                   >  2:538814/1‑149                                                 ATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGC                                                                                  <  2:20270/149‑1                                                     AAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGGAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCC                                                                              >  2:431858/1‑149                                                     AAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTCTTGAAAATCGCAGCC                                                                              >  2:288661/1‑149                                                     AAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCC                                                                              >  1:590487/1‑149                                                      AGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGCAAATCGCAGCCC                                                                             >  1:686132/1‑149                                                           TTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTC                                                                        >  2:555809/1‑149                                                               CGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTCCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCACTCCGTT                                                                    <  1:419032/149‑1                                                                GGGAGAAAAACTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCCTCACGCATTATAGAAAATGGCAGCCCCCCTCCGTgg                                                                   >  1:848291/1‑147                                                                   AGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGAAGCCCCCCTCCGTgttag                                                                >  1:811380/1‑144                                                                     AAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGT                                                              >  2:871640/1‑149                                                                       AAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGTTCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGC                                                            <  2:197728/149‑1                                                                       AAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGC                                                            >  2:837024/1‑149                                                                            CGGCTCAAACATGAAGAAATGAAATGACTGAGCCAGCCGAGAAGAATTTCCCCGCTTAGTCGCACCTTCCTTAAGTAATTGGGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTA                                                       <  2:442656/149‑1                                                                             GGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAG                                                      <  2:50814/149‑1                                                                               CTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGCATGTGAGCGTAGTt                                                    >  1:265867/1‑148                                                                                   AACATGAAGGAATGAAATGACTGAGGCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGA                                                <  1:442002/149‑1                                                                                   AACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGGAATTGAGTGTTTTGTGTGATCTCCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGA                                                >  2:259129/1‑149                                                                                    ACATGAAGAAATGAAATGACTGAGTGAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAAGTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAG                                               >  2:463101/1‑149                                                                                       TGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGCCGAGTAC                                            >  2:227313/1‑149                                                                                               TGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGT                                    <  1:599045/149‑1                                                                                                GAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTC                                   <  2:35198/149‑1                                                                                                        TGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGG                           >  1:586985/1‑149                                                                                                        TGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTACGTCGAGTTAGG                           >  1:203133/1‑149                                                                                                        TGAGACAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGTAGCCCCCCTCCGTTGTATGTGCGTATAGTGACGAGTACAGTTGCGTCGCTTTAGG                           >  1:708239/1‑149                                                                                                                      AGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATA             >  1:402212/1‑149                                                                                                                        AATTTCCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAG           >  2:55464/1‑149                                                                                                                             CCCCGCTTATTCGCACCTTCCTTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAA      >  1:565716/1‑149                                                                                                                               CCGCTTATTCGCACCTTCCTTAAGTAATGGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAAAG    <  1:369230/149‑1                                                                                                                                 GCTTATTCGCACCTTCCTTAAGTAAGTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGAAGCACCCCTCCTTTGTATGTGCGTGTAGTGACGGGTACAGTAGCGTCGATTTAGGAAAAATCTTATATGAGTGTAAAGAC  >  1:387873/1‑149                                                                                                                                                                                                                                                                                       AACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/1391351‑1391495 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTAAGTAATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTTGCGTCGATTTAGGAAAAATCTTAGATAAGTGTAAAGAC  <  CP009273/1972751‑1972620

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.