New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 = 1391495NA (NA)11 (0.570) 9/276 NT 61.1% intergenic (+146/‑127) insH1/ynaJ IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
?CP009273 = 1972751 7 (0.360)intergenic (‑297/‑483) flhD/uspC flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

TAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCG  >  CP009273/1391368‑1391633
                                                                                                                               |                                                                                                                                          
tacaTGGGGAAGAAACGGTCTATTTAGGCTGATTTAAGGCATTTACGGGAGAAAAAAGCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGAt                                                                                                                       <  2:316987/146‑1 (MQ=14)
 aaaTGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACCTAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGAtt                                                                                                                      <  2:7707/149‑1 (MQ=255)
                 gTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATAAAGACATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACGTTCCCGAACTAATCAATGCGTTGATTGTAAATCCAGCTAaga                                                                                                      >  2:127692/1‑149 (MQ=255)
                      aaTAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAgaggtga                                                                                                 <  1:32988/149‑1 (MQ=255)
                             tGATGCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGGATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGAGTTGATTGTAAATCAAGCTAAGAGGTGAGGGTTTc                                                                                          >  2:293808/1‑149 (MQ=18)
                                         tttACGGGCGAAAAAATCGGCTCAAACATGAAGAAATGACATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTACCTAATCCATGCGTTGGTTGTAAATCCAGCACAGAGTCGCGGTCTTCacagagcaggcg                                                                              >  2:280131/1‑141 (MQ=14)
                                            aCGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTTAGAACGGGTAACGGt                                                                           >  2:80603/1‑149 (MQ=18)
                                                  gaAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAAATTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATg                                                                     >  1:170058/1‑149 (MQ=255)
                                                    aaaaaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAATTGTc                                                                   >  2:230297/1‑149 (MQ=255)
                                                       aaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGGAATGTCATg                                                                >  2:238569/1‑149 (MQ=255)
                                                              tCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGt                                                         >  2:80930/1‑149 (MQ=255)
                                                                       aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                                >  2:293695/1‑149 (MQ=255)
                                                                       aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                                >  1:28165/1‑149 (MQ=255)
                                                                          aaatgaaatgACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCAACTTACCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGGGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGGTACGTTTAGGTa                                             >  1:288441/1‑149 (MQ=255)
                                                                                               cGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTAATTATAAATCAAACAAAGAGATGAGGTTTTCAGAGCAGAAAACGGTGAAATGTCATGGTATTGTTACGTATAGGTAACAAGAAATTTGTCTGcacat                        >  1:36438/1‑148 (MQ=38)
                                                                                                               gCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGGTTAGGTAACAAGAGATTTTTCTGCACAAGGAGTACACAATGAtt        >  2:210367/1‑149 (MQ=255)
                                                                                                                     tCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCAAAGAGGTAAGGTTTTCAGAGCAGACAACGATGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAACTTTGTCTGCACAAGGATTACATCATGATTATGGCg  >  1:67788/1‑149 (MQ=255)
                                                                                                                               |                                                                                                                                          
TAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCG  >  CP009273/1391368‑1391633

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.