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

TATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAG  >  USA300TCH1516_ALE/1373492‑1373770                                                                                                                                             |                                                                                                                                           ttgatcttcttaaagctgtttgccaggtaatatgttcccgaagtgccagtctgctgtatgtatgattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaat                                                                                                                                            >  2:65791‑M1/141‑141 (MQ=255) tatTCATTCGTAATGAAATAGATCCTGGAGAATTAGGGGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTT                                                                                                                                            <  1:596836‑M1/141‑1 (MQ=255)  atTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTT                                                                                                                                           <  1:651418‑M1/141‑1 (MQ=255)   ttCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTA                                                                                                                                          >  2:321011‑M1/1‑141 (MQ=255)     tcttctaaaagctgtttgccatttaatattttccctaagtgccagtctgctgtatgtataattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaaTTaaa                                                                                                                                        <  1:423621‑M1/5‑1 (MQ=255)        tctaaaagctgtttgccatttaatattttccctaagtgccagtctgctgtatgtataattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaaTTAAAAcc                                                                                                                                     >  1:221069‑M1/134‑141 (MQ=255)         ctaaaagctgtttgccatttaatattttccctaagtgccagtctgctgtatgtataattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaaTTAAAACCa                                                                                                                                    >  2:87709‑M1/133‑141 (MQ=255)            aaTGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACtt                                                                                                                                 <  1:461170/141‑1 (MQ=255)              tGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTtgt                                                                                                                               <  2:324532/141‑1 (MQ=255)               gAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTtgtg                                                                                                                              <  1:218403/141‑1 (MQ=255)                aaaTAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGa                                                                                                                             >  1:89190/1‑141 (MQ=255)                 aaTAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACATGTGAt                                                                                                                            >  1:611846/1‑141 (MQ=255)                  aTAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTTTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATc                                                                                                                           <  2:254730/141‑1 (MQ=255)                  aTAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATc                                                                                                                           <  1:20247/141‑1 (MQ=255)                    aGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCGGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGa                                                                                                                         <  1:618388/141‑1 (MQ=255)                      aTCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACt                                                                                                                       <  2:242086/141‑1 (MQ=255)                      aTCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACt                                                                                                                       <  1:135688/141‑1 (MQ=255)                       tCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACtt                                                                                                                      >  1:625842/1‑141 (MQ=255)                       tCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACtt                                                                                                                      >  1:625795/1‑141 (MQ=255)                       tCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACtt                                                                                                                      >  2:335792/1‑141 (MQ=255)                        ccTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTc                                                                                                                     <  1:439109/141‑1 (MQ=255)                           ggAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTaa                                                                                                                  <  1:331106/141‑1 (MQ=255)                              gaATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATc                                                                                                               <  2:80602/141‑1 (MQ=255)                                        taagtgccagtctgctgtatgtataattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaaTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAg                                                                                                     >  1:85804‑M1/102‑141 (MQ=255)                                          aTGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTcattgactgatttagaagtcgatcacaagtg                                                                                                   <  2:188081‑M1/141‑32 (MQ=255)                                               cagtctgctgtatgtataattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaaTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGtttt                                                                                              >  1:488703‑M1/95‑141 (MQ=255)                                                agtctgctgtatgtataattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaaTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTa                                                                                             >  1:104834‑M1/94‑141 (MQ=255)                                                   ttattaGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTcattgactgatttagaagtcgatcacaagtggttttaaaa                                                                                          <  2:38044‑M1/141‑41 (MQ=255)                                                   ttattaGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAAtt                                                                                          <  1:295776/141‑1 (MQ=255)                                                        aGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACt                                                                                     <  2:170130/141‑1 (MQ=255)                                                         gCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACtt                                                                                    >  2:142594/1‑141 (MQ=255)                                                                   tGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTcattgactgatttagaagtcgatcacaagtggttttaaaagtaattaattgattaa                                                                          <  1:714401‑M1/141‑57 (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                           >  1:348830/1‑141 (MQ=255)                                                                                                                  aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                           >  1:366562/1‑141 (MQ=255)                                                                                                                  aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                           >  1:187167/1‑141 (MQ=255)                                                                                                                  aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                           >  1:657435/1‑141 (MQ=255)                                                                                                                  aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                           <  1:584536/141‑1 (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)                                                                                                                           ttAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGagtggttttaaaagtaattaattgattaatgttttctttagttttttgtatttatatagcattgctgctctccaaggaacaatca                  <  1:714401‑M2/141‑86 (MQ=255)                                                                                                                                cAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATtat             <  1:211015/141‑1 (MQ=255)                                                                                                                                        taCTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATAcag     <  1:404617/141‑1 (MQ=255)                                                                                                                                          cTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATAcagca   <  1:746194/141‑1 (MQ=255)                                                                                                                                           ttttAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGagtggttttaaaagtaattaattgattaatgttttctttagttttttgtatttatatagcattgctgctctccaaggaacaatcatacagaatgctaataa  <  2:38044‑M2/141‑102 (MQ=255)                                                                                                                                           ttttAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTAATTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATAcagcag  >  1:214745/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                           TATTCATTAGTAATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAG  >  USA300TCH1516_ALE/1373492‑1373770

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.