New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	1929559 =	54 (1.420)	4 (0.110)	4/264	5.6	7.2%	intergenic (‑642/‑526)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
	?	CP000730	1929585 =	52 (1.430)					intergenic (‑668/‑500)	USA300HOU_1794/USA300HOU_1796	hypothetical protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CTTTTTCTTCATCCGATAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAA  >  CP000730/1929449‑1929721                                                                                                                                         |                                                                                                                                         ctTTTTCTTCATCCGATAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCt                                                                                                                                      >  2:9022/1‑141 (MQ=255)    tttCTTCATCCGATAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAgg                                                                                                                                   >  1:54499/1‑141 (MQ=255)      tcttcATCCGATAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCt                                                                                                                                 >  1:58500/1‑141 (MQ=255)          cATCCGATAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTAcc                                                                                                                             >  1:273366/1‑141 (MQ=255)           tttttttAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCTCCTTTTACTAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCa                                                                                                                            >  2:179073/7‑141 (MQ=255)            tCCGATAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCAt                                                                                                                           <  1:398431/141‑1 (MQ=255)             ccGTTAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTCACCAtt                                                                                                                          >  2:25953/1‑141 (MQ=255)                aTAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCAttttt                                                                                                                       <  1:277385/141‑1 (MQ=255)                        tCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATc                                                                                                               <  1:301186/141‑1 (MQ=255)                          ttGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCt                                                                                                                                 >  2:281270/1‑121 (MQ=255)                          ttGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCt                                                                                                                                 <  1:281270/121‑1 (MQ=255)                             gggATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACAGTTTGTAACCGCCATTTACAAACGTGGAAGGTGTGAGATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAAcc                                                                                                          >  1:7098/3‑141 (MQ=255)                             gTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAAcc                                                                                                          >  1:54333/1‑141 (MQ=255)                                  tGAATGTACCCGTGTTTTGATGTTGGTTGATGCATTTTCCTACTGGTTGTAACCGCTATTTACTTTCGTTGGAGGTGTTAATGCATTCTCGCGTATATTTTCATTCCTAGGCTTACCAGTTTTATATTGTCTAGCCGttta                                                                                                     <  2:271873/141‑2 (MQ=255)                                   gAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGt                                                                                                    >  2:216591/1‑141 (MQ=255)                                    aaTGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTa                                                                                                   <  1:214792/141‑1 (MQ=255)                                      tGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTaaa                                                                                                 >  2:89052/1‑140 (MQ=255)                                      tGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAAc                                                                                                 >  1:255532/1‑141 (MQ=255)                                         aCCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTa                                                                                              <  1:308383/141‑1 (MQ=255)                                              tgtTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAActc                                                                                         <  2:58500/141‑1 (MQ=255)                                                    gATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACt                                                                                   >  1:342067/1‑141 (MQ=255)                                                      tGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTaa                                                                                 <  1:165958/141‑1 (MQ=255)                                                         tGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATg                                                                              >  1:21683/1‑141 (MQ=255)                                                         tGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATg                                                                              >  2:49194/1‑141 (MQ=255)                                                          gCTTTATCCATTTTCCTACATTTTATAACCACCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGa                                                                             >  1:218506/1‑141 (MQ=255)                                                            tttATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGAtc                                                                           <  2:338781/141‑1 (MQ=255)                                                             ttATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGAtct                                                                          <  2:33228/141‑1 (MQ=255)                                                                tCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGAtcttct                                                                       <  1:360752/141‑1 (MQ=255)                                                                     tttCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTtctc                                                                  <  1:114017/141‑1 (MQ=255)                                                                           aCATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCa                                                            >  1:149446/1‑141 (MQ=255)                                                                             aTTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCata                                                          <  1:131668/141‑1 (MQ=255)                                                                                  ataACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATCAATTAACTATCTGAACATTAACAAGTGAACTACATAGTCTTCTTTCTTTAGTAATaaaaaa                                                     >  1:140599/1‑141 (MQ=255)                                                                                  ataACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATaaa                                                     >  1:313406/1‑141 (MQ=255)                                                                                  ataACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATaaa                                                     >  1:230993/1‑141 (MQ=255)                                                                                      ccGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCg                                                 <  1:203907/141‑1 (MQ=255)                                                                                       cGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGc                                                >  2:109543/1‑141 (MQ=255)                                                                                              tACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACttt                                         >  2:344933/1‑141 (MQ=255)                                                                                               aCAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCGGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTc                                        <  2:23106/141‑1 (MQ=255)                                                                                                cAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCt                                       >  2:155178/1‑141 (MQ=255)                                                                                                 aaaCGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCtt                                      <  1:170797/141‑1 (MQ=255)                                                                                                  aaCGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTa                                     <  1:291860/141‑1 (MQ=255)                                                                                                    cGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTaaa                                   >  1:194534/1‑141 (MQ=255)                                                                                                      tCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAAtt                                 <  2:173945/141‑1 (MQ=255)                                                                                                          aGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACa                             >  2:303517/1‑141 (MQ=255)                                                                                                           ggTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACaa                            <  2:318732/141‑1 (MQ=255)                                                                                                               tgAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATc                        <  1:186271/141‑1 (MQ=255)                                                                                                                gAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCt                       <  2:109236/141‑1 (MQ=255)                                                                                                                   aTCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTAtt                    >  2:120504/1‑141 (MQ=255)                                                                                                                      atacgcgagTATGATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATtctc                 >  1:401705/9‑141 (MQ=255)                                                                                                                      aTACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATtctc                 >  1:396564/1‑141 (MQ=255)                                                                                                                       tACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCa                >  1:6104/1‑141 (MQ=255)                                                                                                                       tACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCCCa                >  1:117377/1‑141 (MQ=255)                                                                                                                                ataATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTg       <  2:186889/141‑1 (MQ=255)                                                                                                                                   aTTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTcc    <  1:337305/141‑1 (MQ=255)                                                                                                                                     ttCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCaa  <  1:216591/141‑1 (MQ=255)                                                                                                                                     ttCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCaa  >  2:216677/1‑141 (MQ=255)                                                                                                                                         |                                                                                                                                         CTTTTTCTTCATCCGATAAGTTATCTTGGTGATTGAATGTACCCGTGTTTTGATGTTGCTTTATCCATTTTCCTACATTTTATAACCGCCATTTACAAACGTCGAAGGTGTGAAATCATACTCGCGTATAATTTCATTCCTAGGCTTACCATTTTTATATAATCTAACCATTTGTAACTTAAACTCTGAACTAAATGATCTTCTTTCTCTTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAA  >  CP000730/1929449‑1929721

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