New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 37094 =41 (1.290)3 (0.100) 3/240 NT 6.8% coding (21/231 nt) USA300HOU_0028 hypothetical protein
?CP000730 37188 = 45 (1.530)coding (115/231 nt) USA300HOU_0028 hypothetical protein

AACATATAAGATAGAGAAATAAACTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATTATA  >  CP000730/36955‑37229
                                                                                                                                           |                                                                                                                                       
aacgtacctcttatctgtaattttactgagaactgcttttaacaaacctcttatctgcaattttacttagaattgcttttactattcctcttattagtataatctcagtaagaatgcgtataaaaatgaaaattacaacCg                                                                                                                                        <  2:270482‑M1/2‑1 (MQ=255)
        aGAAAGAGAAATAAACTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTa                                                                                                                                <  2:314895/141‑1 (MQ=255)
               gaAATAAACTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCAt                                                                                                                         >  1:212314/1‑141 (MQ=255)
                      aCTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTTcc                                                                                                                  >  2:347205/1‑141 (MQ=255)
                      aCTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGcc                                                                                                                  >  2:339266/1‑141 (MQ=255)
                                    gtgCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCtg                                                                                                    >  2:166804/1‑140 (MQ=255)
                                           atgaGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCAt                                                                                             <  1:296322/141‑1 (MQ=255)
                                               gCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGATTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGAATGGCTGGGGCAGTTAGt                                                                                         >  1:123932/1‑141 (MQ=255)
                                               ctcttatctgcaattttacttagaattgcttttactattcctcttattagtataatctcagtaagaatgcgtataaaaatgaaaattacaacCGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGt                                                                                         >  2:63504‑M1/93‑141 (MQ=255)
                                                cTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATCTTTTCCGTGTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGtc                                                                                        <  1:187977/141‑1 (MQ=255)
                                                  tGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGtctc                                                                                      <  2:284244/141‑1 (MQ=255)
                                                  tGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGATAGAAGTTGATTATGGCTCGAGCCATTAGtctc                                                                                      <  1:392355/141‑1 (MQ=255)
                                                  tGGGACACAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGtctc                                                                                      <  2:221400/141‑1 (MQ=255)
                                                   gggTCATAAATCATACCGCGACATTAATAAGCATATCACTAACCTGATGTTTCAAAGTTTACAGTGATATGCTTATTTTGTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGtctct                                                                                     <  2:13869/141‑1 (MQ=255)
                                                              ccTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTa                                                                          >  1:270482/1‑141 (MQ=255)
                                                               cTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTAt                                                                         >  1:117587/1‑141 (MQ=255)
                                                                   cTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTccc                                                                     >  2:314009/1‑141 (MQ=255)
                                                                   cTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTccc                                                                     >  1:47164/1‑141 (MQ=255)
                                                                      gAAATAAATAAGCATATCACTAAACTGAGTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGTACATACTATTCCCtag                                                                  >  1:331355/1‑139 (MQ=255)
                                                                                    tatCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTTCTAGTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTa                                                    <  1:109802/141‑1 (MQ=255)
                                                                                                gATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTTTGTGTCTCCTTGCCTAGGGGTATGGGTTGAGTCATCCGTCTTGCGCACAGAGGATTTCGTCATGGTGCTGCACGTACAAAATCGGTTg                                        >  2:34212/1‑141 (MQ=255)
                                                                                                gATTTTTTAAAGGTTACAGGGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTg                                        <  2:75146/141‑1 (MQ=255)
                                                                                                     tttAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAAtt                                   >  1:376366/1‑141 (MQ=255)
                                                                                                     tttAAAGGTTACAGTGATATGCTTATTTTTTTATCTTACGAGTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAAtt                                   <  1:149055/141‑1 (MQ=255)
                                                                                                      ttAAAAGTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAAttt                                  <  2:121708/141‑1 (MQ=255)
                                                                                                          aGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCAt                              >  1:23970/1‑141 (MQ=255)
                                                                                                            tttACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCAttt                            <  1:46420/141‑1 (MQ=255)
                                                                                                            taagaatgcgtataaaaatgaaaattacaacCGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCAttt                            <  2:55175‑M1/110‑1 (MQ=255)
                                                                                                              tACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCAttttt                          >  1:42534/1‑141 (MQ=255)
                                                                                                                cAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATTCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTtat                        <  1:369184/141‑1 (MQ=255)
                                                                                                                 aGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTtata                       <  1:30/141‑1 (MQ=255)
                                                                                                                   tGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACg                     <  1:106932/141‑1 (MQ=255)
                                                                                                                   ggATATGCTTACTCTTCTAGCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACg                     <  1:148527/140‑1 (MQ=255)
                                                                                                                    gATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGc                    <  1:79369/141‑1 (MQ=255)
                                                                                                                    gATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGc                    >  1:341830/1‑141 (MQ=255)
                                                                                                                      tatGCTTATTTTTTTATCTTACGATTTTGGACGTGCATGCCTGCCTCGGGGTATGGCTCGAGCCATTAGTCTCTCTCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCAt                  <  2:132671/141‑1 (MQ=255)
                                                                                                                          cTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCtt              <  1:318880/141‑1 (MQ=255)
                                                                                                                          cTTATTTTCTTATCTTACTATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCtt              <  1:155325/141‑1 (MQ=255)
                                                                                                                           aaatgaaaattacaacCGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTa             >  1:55175‑M1/17‑141 (MQ=255)
                                                                                                                             aTTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACt           <  2:70962/141‑1 (MQ=255)
                                                                                                                              tttttttATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTg          <  1:166804/141‑1 (MQ=255)
                                                                                                                               ttttttATCTTACGATTTTGTACGGGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTga         <  1:91896/141‑1 (MQ=255)
                                                                                                                                  tttATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGAt      >  2:277866/1‑141 (MQ=255)
                                                                                                                                  tttATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATAGGTTGTCATTTTCATTTTTATAAGCCTTCTTACTGAGAt      >  1:58792/1‑141 (MQ=255)
                                                                                                                                     aTCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATtat   <  1:314009/141‑1 (MQ=255)
                                                                                                                                      tCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATtata  <  2:113774/141‑1 (MQ=255)
                                                                                                                                      tCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATtata  >  1:236937/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                       
AACATATAAGATAGAGAAATAAACTAGTGGCCGATTGTGCTTGATGAGCTTGGGACATAAATCCTAACTCGAAATAAATAAGCATATCACTAAACTGATTTTTTAAAGTTTACAGTGATATGCTTATTTTTTTATCTTACGATTTTGTACGTGCATGCTTGCCTAGGGGTATGGCTCGAGCCATTAGTCTCTCGCACATACTATTCCCTCAGGCGTCAGCACTTACAAAATCGGTTGTAATTTTCATTTTTATACGCATTCTTACTGAGATTATA  >  CP000730/36955‑37229

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.