New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1373632 =	46 (1.000)	3 (0.070)	3/238	NT	6.9%	intergenic (+7/‑117)	USA300TCH1516_01283/sbcD	hypothetical protein/Nuclease SbcCD subunit D
	?	USA300TCH1516_ALE	1373681 =	39 (0.920)					intergenic (+56/‑68)	USA300TCH1516_01283/sbcD	hypothetical protein/Nuclease SbcCD subunit D

TTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAATATTAAATGGCAAACAGCTTTTAGAAGATCAA  >  USA300TCH1516_ALE/1373542‑1373820                                                                                                                                            |                                                                                                                                            ttattaGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAAtt                                                                                                                                            <  1:295776/141‑1 (MQ=255)      aGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACt                                                                                                                                       <  2:170130/141‑1 (MQ=255)       gCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACtt                                                                                                                                      >  2:142594/1‑141 (MQ=255)                             ggAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCCATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATAtt                                                                                                                <  2:74629/141‑1 (MQ=255)                             ggAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATAtt                                                                                                                <  1:105366/141‑1 (MQ=255)                               agagCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATtaa                                                                                                              <  1:255733/141‑1 (MQ=255)                               agagCAGCAATGCTATATAAATAAAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATtaa                                                                                                              <  1:169747/141‑1 (MQ=255)                                   cagcaATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATtaaaata                                                                                                          >  1:499005/1‑141 (MQ=255)                                     gcaATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATtaaaataaa                                                                                                        <  2:303585/141‑1 (MQ=255)                                       aaTGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAg                                                                                                      <  1:553095/141‑1 (MQ=255)                                       aaTGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAg                                                                                                      <  1:440102/141‑1 (MQ=255)                                           cTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGaa                                                                                                  <  1:734546/141‑1 (MQ=255)                                                 aaaTACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATg                                                                                            >  2:50804/1‑141 (MQ=255)                                                   aTACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGtt                                                                                          <  2:245607/141‑1 (MQ=255)                                                   aTACAAAAAACTAAAGAAAACATTAATCAATTAATCACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGtt                                                                                          >  1:688294/1‑141 (MQ=255)                                                         aaaaCTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTatat                                                                                    <  2:31764/141‑1 (MQ=255)                                                          aaaCTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCTACTTCTAACTCAGTCAATGAGTGGTTTTAATTTTACTAGAAAAGGATAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTAGATg                                                                                   >  1:71006/1‑141 (MQ=255)                                                            aCTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGa                                                                                 <  1:109313/141‑1 (MQ=255)                                                              tAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAgg                                                                               <  1:757218/141‑1 (MQ=255)                                                               aaaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGc                                                                              <  1:492285/141‑1 (MQ=255)                                                                aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                                                             >  1:187167/1‑141 (MQ=255)                                                                aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                                                             <  1:584536/141‑1 (MQ=255)                                                                aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                                                             >  1:657435/1‑141 (MQ=255)                                                                aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                                                             >  1:366562/1‑141 (MQ=255)                                                                aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                                                             >  1:348830/1‑141 (MQ=255)                                                                   aaaaCATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTa                                                                          >  2:298424/1‑141 (MQ=255)                                                                      tcATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATg                                                                       <  2:244630/140‑1 (MQ=255)                                                                      aCATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATg                                                                       <  1:206450/141‑1 (MQ=255)                                                                       cATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAAAGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGa                                                                      <  2:257098/141‑1 (MQ=255)                                                                              cAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATtat                                                               <  1:211015/141‑1 (MQ=255)                                                                                      taCTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATAcag                                                       <  1:404617/141‑1 (MQ=255)                                                                                        cTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATAcagca                                                     <  1:746194/141‑1 (MQ=255)                                                                                         ttttAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTAATTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATAcagcag                                                    >  1:214745/1‑141 (MQ=255)                                                                                            taaaaccactcattgactgatttagaagtcgatcacaagtggttttaaTTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACt                                                 >  1:104834‑M2/49‑141 (MQ=255)                                                                                            TAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACt                                                 >  1:25045‑M1/1‑141 (MQ=255)                                                                                            TAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACt                                                 >  2:293929‑M1/1‑141 (MQ=255)                                                                                             aaaaccactcattgactgatttagaagtcgatcacaagtggttttaaTTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTg                                                >  1:488703‑M2/48‑141 (MQ=255)                                                                                             AAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGGACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTg                                                <  1:743078‑M1/141‑1 (MQ=255)                                                                                                    ctcattgactgatttagaagtcgatcacaagtggttttaaTTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTa                                         >  1:85804‑M2/41‑141 (MQ=255)                                                                                                    CTTGTGTTCGACGGCGAAATCAGTCAAGGAGTATTTGTGGTGTGATTTGAAAAGGTGAGATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTa                                         >  1:748985‑M1/1‑141 (MQ=255)                                                                                                    CTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTa                                         <  2:47684‑M1/141‑1 (MQ=255)                                                                                                    CTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTa                                         <  1:457768‑M1/141‑1 (MQ=255)                                                                                                      tgtgATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAgg                                       <  1:640992/141‑1 (MQ=255)                                                                                                       gtgATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAggg                                      <  2:64118/141‑1 (MQ=255)                                                                                                            cGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAat                                 >  1:267136/1‑141 (MQ=255)                                                                                                                   tAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATAGTGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAATATTAAAt                          >  1:745976/1‑141 (MQ=255)                                                                                                                        cAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATGTGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAATATTAAATGGCaa                     <  2:309672/141‑1 (MQ=255)                                                                                                                          gTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGATGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAATATTAAATGGCAAAc                   <  1:464842/141‑1 (MQ=255)                                                                                                                          gTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATGCAGCAGACTGGCACTTAGGGAAAATATTAAATGGCAAAc                   >  1:582410/1‑141 (MQ=255)                                                                                                                                gAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAATATTAAATGGCAAACAGCttt             <  1:574299/141‑1 (MQ=255)                                                                                                                                   tggttttaaTTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAATATTAAATGGCAAACAGCTTTTag          >  2:87709‑M2/10‑141 (MQ=255)                                                                                                                                    ggttttaaTTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAATATTAAATGGCAAACAGCTTTTaga         >  1:221069‑M2/9‑141 (MQ=255)                                                                                                                                       tttaaTTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAATATTAAATGGCAAACAGCTTTTagaaga      <  1:423621‑M2/136‑1 (MQ=255)                                                                                                                                           aTTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATCATACATACAGCAGACTGGCACTTCGGGAACATATTACCTGGCAAACAGCTTTAAGAAGATCaa  >  2:65791‑M2/2‑141 (MQ=255)                                                                                                                                            |                                                                                                                                            TTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTAGGGAAAATATTAAATGGCAAACAGCTTTTAGAAGATCAA  >  USA300TCH1516_ALE/1373542‑1373820

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.