New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 = 244282146 (0.880)5 (0.110) 5/228 NT 11.3% intergenic (+18/+40) USA300HOU_2304/USA300HOU_2305 transcriptional regulator/hypothetical protein
?CP000730 = 2442838 38 (0.830)intergenic (+35/+23) USA300HOU_2304/USA300HOU_2305 transcriptional regulator/hypothetical protein

AACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCTAAATTAGTAA  >  CP000730/2442698‑2442976
                                                                                                                                            |                                                                                                                                          
aaCTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCt                                                                                                                                            >  2:357726/1‑141 (MQ=255)
  ctgctcgTACAGCTTATTCTAGCTTCATCAGGTATTATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCATATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTAt                                                                                                                                          <  2:173295/135‑1 (MQ=255)
          aCAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataaatt                                                                                                                                  <  1:576655‑M2/141‑11 (MQ=255)
               cTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATACTGCGTATTTACTACATAAAGAATTATCAAATTAGAAAAAAGGAAGTTATGATTTACTGGCCTTGAGCCTatcataacttccttt                                                                                                                             <  2:218520‑M2/141‑16 (MQ=255)
                  ttttAGCTTCATAAGGAATGATAGAGTCTTGGAAACACTTATAGGAAAAGTTAATGAGTATTTTCCACATATTGATATTAAAAAAAAAAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTAt                                                                                                                          <  2:103404/138‑1 (MQ=255)
                  ttCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTAt                                                                                                                          <  1:300020/141‑1 (MQ=255)
                    cTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAACAATAATGTTTTTGTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCa                                                                                                                        <  1:114966/141‑1 (MQ=255)
                     tAGTTTCATCAGTTATCTTATCTTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTCTGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCAt                                                                                                                       <  1:75936/141‑1 (MQ=255)
                       gCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCAttt                                                                                                                     >  1:490120/1‑141 (MQ=255)
                       gCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCAttt                                                                                                                     <  2:317977/141‑1 (MQ=255)
                          tcatcaGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTAt                                                                                                                  <  2:391017/141‑1 (MQ=255)
                            atcaGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTAttg                                                                                                                <  2:543924/141‑1 (MQ=255)
                                 ttATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATtgttgtg                                                                                                           <  1:573287/141‑1 (MQ=255)
                                    tCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCCTGAGCCTATCATAACTTCCTTTTATCCTTTTAttgttttgttt                                                                                                        >  1:587052/1‑140 (MQ=255)
                                     tcactatttctacaaaCACTTTTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTTCTTTTATCATTTTATTGTTGTGTTGa                                                                                                       <  1:135342/128‑1 (MQ=255)
                                              tttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGAt                                                                                              <  1:217514/141‑1 (MQ=255)
                                               ttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataacttccttttttctaatttgaaatatcattatgtagtaaat                                                                                             <  1:156228‑M2/141‑48 (MQ=255)
                                               ttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATa                                                                                             >  2:561322/1‑141 (MQ=255)
                                                tGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGAtga                                                                                            >  2:81844/1‑139 (MQ=255)
                                                tGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATat                                                                                            >  1:175182/1‑140 (MQ=255)
                                                 gAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAAc                                                                                           <  1:183122/141‑1 (MQ=255)
                                                    acacTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTGTCGATAACTTg                                                                                        >  2:475825/1‑141 (MQ=255)
                                                       cTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGCTa                                                                                     >  2:445538/1‑141 (MQ=255)
                                                         tGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTCCa                                                                                   >  2:149744/1‑141 (MQ=255)
                                                          gTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACAt                                                                                  <  1:599294/141‑1 (MQ=255)
                                                           tAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATc                                                                                 <  2:77853/141‑1 (MQ=255)
                                                                   tataATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCaaa                                                                         >  2:253477/1‑141 (MQ=255)
                                                                             aTTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataacttccttttttctaatttgaaatatcattatgtagtaaatactcattatattttcttacaagtgtttcaa                                                               >  2:156228‑M2/1‑64 (MQ=255)
                                                                             aTTTACTACATAATGAAATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCg                                                               <  1:76824/141‑1 (MQ=255)
                                                                              tttACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGa                                                              <  1:357726/141‑1 (MQ=255)
                                                                              tttACTACATAATGATATTTAAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGa                                                              <  2:91942/141‑1 (MQ=255)
                                                                                 actacATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAAc                                                           >  2:267555/1‑141 (MQ=255)
                                                                                  ctaaATAAAGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAACCGCTTATCACTTCCTTTTATCATTTTATTATTGTGTTGATATTTCGATAACGTTGTACATCTTCTCAAACATCAATTCGataac                                                          >  2:155419/1‑137 (MQ=255)
                                                                                   tacATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCa                                                         <  1:49443/141‑1 (MQ=255)
                                                                                       tAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataacttcttttttctaatttgaaatatcattatgtaataaatactcattatatttttttacaagtgtttcaaagaatatatga                                                     <  2:31997‑M2/141‑88 (MQ=255)
                                                                                            atatTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATg                                                >  2:461397/1‑141 (MQ=255)
                                                                                            atatTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATg                                                >  2:602189/1‑141 (MQ=255)
                                                                                                   aaaTTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCGCCATGTcatcat                                         >  1:71798/1‑141 (MQ=255)
                                                                                                        aGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGatat                                    >  1:596631/1‑141 (MQ=255)
                                                                                                        aGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCGTATATCATTTTATTGTTGTGTTGATGCTTCGATAACGTGGTACATCTTATAAAACAGCAATTCGAAACCATGCACCCTCGCACCATGatat                                    >  2:478350/1‑141 (MQ=255)
                                                                                                          aaaaaaGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttc                                  <  1:101518/141‑1 (MQ=255)
                                                                                                          aaaaaaGGAAGTTATGATTGAATGGCCTTGAGACTatcataacttccttttttctaatttgaaatatcattatgtagtaaatactccttatattttcttacaagggtttcaaggtatatatgataactaatggagctagaa                                  <  2:272561‑M2/141‑107 (MQ=255)
                                                                                                           aaaaaGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttct                                 >  2:485592/1‑141 (MQ=255)
                                                                                                            aaaaGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttctt                                >  2:113307/1‑141 (MQ=255)
                                                                                                                  aaGTTATTATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttcttttttct                          <  1:179595/141‑1 (MQ=255)
                                                                                                                   aGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGGGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttcttttttctt                         >  1:327620/1‑141 (MQ=255)
                                                                                                                      tATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTg                      <  1:580207/141‑1 (MQ=255)
                                                                                                                       aTGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGc                     <  1:74251/141‑1 (MQ=255)
                                                                                                                            ttAATGGCCTTGAGCCTatcataacttccttttatataatttgaaatatcattatgtaataaatactcattatattttcttacaagtgtttcaaagaatatatgataactgataaagctagaatggtcggtaccattagtt                <  1:40815‑M2/141‑125 (MQ=255)
                                                                                                                                tGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCt            >  2:390530/1‑141 (MQ=255)
                                                                                                                                 ggCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCTa           <  1:267555/141‑1 (MQ=255)
                                                                                                                                          ccTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCTAAATTAGTaa  <  2:540765/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                          
AACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCTAAATTAGTAA  >  CP000730/2442698‑2442976

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.