New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2660570 =43 (0.930)4 (0.100) 4/234 NT 9.9% intergenic (+12/+237) ddh/USA300HOU_2514 D‑lactate dehydrogenase/HAD superfamily hydrolase
?CP000730 2660603 = 34 (0.810)intergenic (+45/+204) ddh/USA300HOU_2514 D‑lactate dehydrogenase/HAD superfamily hydrolase

CTGATGAAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATATTTGATGA  >  CP000730/2660467‑2660737
                                                                                                                                        |                                                                                                                                      
ctGATGAAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGTCATGTGCCTTTGCTTTTTAtt                                                                                                                                     <  1:282748/140‑1 (MQ=255)
  gatgaAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAAGATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTAtttt                                                                                                                                   >  2:376829/1‑140 (MQ=255)
   atgaAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTg                                                                                                                                  >  2:51493/1‑140 (MQ=255)
    tgaAGCAGTACAAAACCTTGTTGAAGGTGGTTGAAACGTAGCTTTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATCTTGt                                                                                                                                 <  1:374236/140‑1 (MQ=255)
       aGCAGTACAAAACCTTATTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTTAAAAACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCATTTGATTTTTATTTTGtata                                                                                                                              >  1:292967/1‑140 (MQ=255)
          aGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCt                                                                                                                           >  1:60913/1‑140 (MQ=255)
            tACACAGCCGTGTTGAAGGTGTTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGt                                                                                                                         <  2:154892/140‑1 (MQ=255)
            tACAAAACCTTGGTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGt                                                                                                                         <  2:154908/140‑1 (MQ=255)
                aaaCCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGGTTTTTATTTTGTATATCTGTATCa                                                                                                                     >  2:55085/1‑140 (MQ=255)
                 agccTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGGATATCTGtcgcat                                                                                                                    <  2:93576/138‑6 (MQ=255)
                   tcTTGTTGAAGTGGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGTAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCaaaa                                                                                                                  <  2:319387/139‑1 (MQ=255)
                    cTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAAt                                                                                                                 <  1:549505/140‑1 (MQ=255)
                     ttgttgAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTCAATGAAGACGCACACCTTGTGCCTTTGCTTTTTATTTTGTATATCTGTATCACAATc                                                                                                                >  1:483138/1‑140 (MQ=255)
                     ttgttgAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAACAta                                                                                                                >  2:135075/1‑139 (MQ=255)
                     ttgttgAAGGTGGTATAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTCTTTTGTATATCTGtctacaaatt                                                                                                                >  2:135312/1‑131 (MQ=255)
                        ttgAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGAt                                                                                                             <  1:528291/140‑1 (MQ=255)
                            actaaaatcatttgaatagatgataaaataaagcggattttaatcaaatcgattttgatacagatatacaaaataaaaagcaaaggcgcgccatgtgcctttgctcttTATTTTGTATATCTGTATCAAAATCGATTTGa                                                                                                         <  1:348878‑M2/32‑1 (MQ=255)
                              taaattcatttgaatagataataaaattaagcggattctaatcaaatcgattttgatacatatatacaaaataaaaatcaaatgcacatggcgcgcctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGAtt                                                                                                       <  2:180755‑M2/34‑1 (MQ=255)
                               tggtTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTa                                                                                                      <  1:109315/140‑1 (MQ=255)
                                tgtTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTaa                                                                                                     <  1:363822/139‑1 (MQ=255)
                                 gtTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTaaa                                                                                                    <  2:67267/140‑1 (MQ=255)
                                    tAAACGCAGCCTTATCTGTCATTAACACTGGTACAAAGGATACACGGTTACATTGTCATAGACATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCAATTTGATTAAAATc                                                                                                 >  1:129298/1‑140 (MQ=255)
                                    tAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAACAAAAGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATc                                                                                                 >  1:280270/1‑140 (MQ=255)
                                             caTTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATTTTTTTAATAGCTTTGGCGCGCCTTGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCtttatt                                                                                        <  1:197282/140‑1 (MQ=255)
                                                         ttAACACTGGTACATGGGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTAtt                                                                            <  2:79803/140‑1 (MQ=255)
                                                          tAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTc                                                                           >  2:445745/1‑140 (MQ=255)
                                                                    aCAGGTGAAACACGTTTAAATCAATTTATATATTTAAAAGCAAAGGCGCGCCATTTGTCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCACCTATTCAAATGAtttt                                                                 <  1:283198/140‑1 (MQ=255)
                                                                     aatcaaatcgattttgatacagatatacaaaataAAAAGCAAAGGCGCGCCATGTGCATTTGATTTTTATTTTGTATATATGTATCAAAATCGATTTGATTAGAATCCGCTTAATTTTATTATCTATTCAAATGAATTTa                                                                <  2:180755‑M1/106‑1 (MQ=255)
                                                                       tcaaatcgattttgatacagatatacaaaataAAGAGCAAAGGCACATGGCGCGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGt                                                              <  1:348878‑M1/108‑1 (MQ=255)
                                                                        gtgAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTTTTTTATCTTGTATTCAAATGATTTTAGTg                                                             >  2:247841/1‑140 (MQ=255)
                                                                            atcacGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGTCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCt                                                         <  1:81267/138‑1 (MQ=255)
                                                                            aaCACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCt                                                         >  1:31035/1‑140 (MQ=255)
                                                                               acGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTAt                                                      <  1:458455/140‑1 (MQ=255)
                                                                               acGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTAt                                                      >  1:330842/1‑140 (MQ=255)
                                                                                 gTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTAttt                                                    >  1:276675/1‑140 (MQ=255)
                                                                                        ttAATATATATATTTAAAACCAAAGGCGCGCCATTTCCTTTTGCTTTTTATTTTGTATATCTTCATCAAAATCGATTTGCTTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATg                                             <  2:236943/140‑1 (MQ=255)
                                                                                                   atTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGcc                                  <  2:63352/140‑1 (MQ=255)
                                                                                                         aggcaaaggcacatggctcgtctttgtttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCt                            <  2:348878‑M2/109‑1 (MQ=255)
                                                                                                         AAGCAAAGGCGTGCCATGTGCTTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCt                            >  1:41305‑M1/1‑140 (MQ=255)
                                                                                                          AGCAAGGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATTTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTGAGTGCGGTTATTTTACTATGGCATTAGTGCCTAACCTg                           >  1:13576‑M1/1‑140 (MQ=255)
                                                                                                           GCAAAGGCGCGCCATGTGCCTTTTCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGt                          >  1:51493‑M1/1‑140 (MQ=255)
                                                                                                            CAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGtt                         <  1:484242‑M1/140‑1 (MQ=255)
                                                                                                               AGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAAGCTGTTTga                      <  2:211960‑M1/140‑1 (MQ=255)
                                                                                                                 GCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTgaga                    <  2:110056‑M1/140‑1 (MQ=255)
                                                                                                                   acatggcgcgcctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGata                  >  2:362677‑M2/22‑140 (MQ=255)
                                                                                                                    cgcCATGTGCCTTTGCTTTTTATTTTGTATATCTGTCTCATAATCGATATGATTATAATCCGGTTTATTTTATCATCTATTCAAATGCTTTTAGGTCGCTTATTTTACTATGGCCTTATTGCCTAACCTGTTTGAGatat                 >  2:227647/1‑140 (MQ=255)
                                                                                                                    cgcCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGatat                 >  1:471109/1‑140 (MQ=255)
                                                                                                                             cctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGTTTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATAtt        <  1:199709‑M2/129‑1 (MQ=255)
                                                                                                                             cctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATAtt        <  2:521241‑M2/129‑1 (MQ=255)
                                                                                                                             cctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTACCATCTATTCAAATGATTTTATTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATAtt        <  2:442575‑M2/129‑1 (MQ=255)
                                                                                                                                   cttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATATTtgttga  >  2:506494‑M2/6‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                      
CTGATGAAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATATTTGATGA  >  CP000730/2660467‑2660737

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.