New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 800928	83 (0.960)	8 (0.100)	5/282	6.6	11.0%	intergenic (+62/‑289)	hisC_1/USA300HOU_RS03915	Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase
	?	USA300TCH1516_ALE	801948 =	51 (0.620)					intergenic (+189/+435)	USA300HOU_RS03915/USA300HOU_RS03920	Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATAAAGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCTTTATCATTTCCGTCC  >  USA300TCH1516_ALE/801807‑802095                                                                                                                                              |                                                                                                                                                    ataAAGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGaa                                                                                                                                              >  1:615503/1‑149 (MQ=255)  taAAGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGaaa                                                                                                                                             <  2:324375/149‑1 (MQ=255)   aaaGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATAATCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAAt                                                                                                                                            >  1:180235/1‑149 (MQ=255)   aaaGTAATAGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGaaaa                                                                                                                                            >  1:937163/1‑148 (MQ=255)    aaGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAGTTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATa                                                                                                                                           >  2:633222/1‑149 (MQ=255)    aaGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACACCAATTTCTACAGACAAGCGAAGTTGGGATGCGACCCAACCTAAAGAAATa                                                                                                                                           >  2:460747/1‑149 (MQ=37)       tagttGTGCCTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGCGAACTTGGAACGACAATTTCTACAGCCAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATAAtt                                                                                                                                        >  2:472487/4‑149 (MQ=38)          ttGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACttttt                                                                                                                                     <  2:252406/149‑1 (MQ=255)            gtgACTGAGATGAACTTTTGTGTCTTCGACACTACAACACTATATTGGCCGGAGTTGAGTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGGAAGGTGGGGGGGGCCCCACCATAAAGAGATAcctgttgt                                                                                                                                   >  2:120850/1‑142 (MQ=21)            gtgACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGCCAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCt                                                                                                                                   >  2:723986/1‑149 (MQ=255)            gtgACTGAGATGAACTTTTATGTCTTAGACACTACAACACGATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGAGGGCCCCAGCATAAAGAAATACTTTTTCt                                                                                                                                   <  1:481573/149‑1 (MQ=255)              gACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTCCGGGTCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCttt                                                                                                                                 <  1:677138/149‑1 (MQ=255)              gACTGAGATGAACTTTGATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCttt                                                                                                                                 <  1:59491/149‑1 (MQ=255)                cTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGCTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAg                                                                                                                               >  1:254172/1‑149 (MQ=255)                     gtGAACTTTTAGGTCTTAGAAACTACCACACTATCGTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAAGTTCTACAGACAATGCAAGTTGGGGTGGGCCTCAACATAAAGAAATACTTTTTCTTTAGAAAtt                                                                                                                          <  2:345088/148‑1 (MQ=21)                     aTGAACTTTTATGTCGTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGATAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAAtt                                                                                                                          <  2:23827/149‑1 (MQ=255)                      tGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTa                                                                                                                         <  1:762546/149‑1 (MQ=255)                               ttGTCTTAGCAACTACAACACTATATTGGCAGTAGTTGAATGCGGGGCCCCAACATAGAGAAATTGGATCGCCAATTTCTACAGACAATGCAAGTTGGTGTGGGTCCCAACATAAAGAACTACTTTTTCTTTAGAAATTAGTATTTCtt                                                                                                                <  1:238149/148‑1 (MQ=18)                                  tCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATg                                                                                                             >  1:817997/1‑149 (MQ=255)                                   cTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGc                                                                                                            >  1:818462/1‑149 (MQ=255)                                       gACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGa                                                                                                        >  2:118783/1‑149 (MQ=255)                                          acTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAgtg                                                                                                     <  1:923088/149‑1 (MQ=255)                                          acTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAAACTAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGGGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAgtg                                                                                                     <  1:79770/149‑1 (MQ=255)                                           cTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTTTTATGCATGAgtgt                                                                                                    >  2:727829/1‑149 (MQ=255)                                              caacaCTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGGAATTAGTATTTCTTATGCATGAGTGTaaa                                                                                                 >  1:500077/1‑148 (MQ=255)                                                          ggCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCat                                                                                     <  1:735403/149‑1 (MQ=255)                                                            cAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCGTGAATTCatct                                                                                   >  2:207844/1‑147 (MQ=255)                                                            cAGTAGTTGACTGCGGGGCCCCAACAGAGAGAACTTGGAACGCCAATTTCTACAGACAATGCAAGTTGGTGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCatat                                                                                   <  1:608629/149‑1 (MQ=255)                                                                agtTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATAttttt                                                                               >  1:822783/1‑149 (MQ=255)                                                                   tGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAg                                                                            >  1:929018/1‑149 (MQ=255)                                                                   tGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGGAACTCATGCATTCATATTTTTAAg                                                                            >  1:396248/1‑149 (MQ=255)                                                                      cTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTac                                                                         <  2:482977/149‑1 (MQ=255)                                                                      cTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTac                                                                         <  2:256143/149‑1 (MQ=255)                                                                           gggCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACAtt                                                                    >  1:853038/1‑149 (MQ=255)                                                                           gggCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACAtt                                                                    >  1:106558/1‑149 (MQ=255)                                                                                         agaAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATg                                                      >  2:288144/1‑149 (MQ=255)                                                                                            aaTTGGAACCCCAATTTCTACATACAAATCAAATTGGGGTGGGCCCCAACATAAAGAAATACTTGTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATa                                                   <  2:131251/149‑1 (MQ=18)                                                                                                 gAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTACCCCCTGCCTTAAGCTTTTTAAGTACACATTGGATGTGACTAATGATAAAgca                                              >  1:582854/1‑147 (MQ=18)                                                                                                  aaCGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAAt                                             >  2:820113/1‑149 (MQ=255)                                                                                                    cgctcaTTTCGACAGACAATGCAAGTTGGGGTGTGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATCTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCg                                           <  1:494119/144‑1 (MQ=255)                                                                                                      ccAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAAAATCGCt                                         >  1:837937/1‑149 (MQ=255)                                                                                                       cAATTTCGACAGACAATGCAAGTTGGGGTGGGCCCGAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTa                                        <  2:787711/149‑1 (MQ=255)                                                                                                            tCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATaa                                   <  1:346279/149‑1 (MQ=255)                                                                                                                cAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATaatcaa                               <  1:380028/149‑1 (MQ=255)                                                                                                                 aGACCATGCAAGGTGGGGTGGTACCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATaatcaat                              <  2:587108/149‑1 (MQ=255)                                                                                                                         cAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTCCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATGGCTACATTATCAATCACTAGTc                      >  2:603105/1‑149 (MQ=255)                                                                                                                         cAAGTTGGGGAGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATGTTTAAGTCTACATTAGCTGTGACTAATGATAAAATATCGCTACATAATCCATCATTAGTc                      >  2:534521/1‑149 (MQ=18)                                                                                                                          aaGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATAAATCATTGGTCg                     >  2:30142/1‑149 (MQ=255)                                                                                                                            gTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGtt                   <  1:213468/149‑1 (MQ=255)                                                                                                                                gggTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCttt               <  1:812042/149‑1 (MQ=255)                                                                                                                                   tGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCTTTATc            >  1:622937/1‑149 (MQ=255)                                                                                                                                           aaaaTAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCTTTATCATTTCCGt    <  2:107380/146‑1 (MQ=255)                                                                                                                                             cATAAAGAAATACTGTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACCCATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCTTTATCATTTCCGTcc  <  1:309773/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                    ATAAAGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCTTTATCATTTCCGTCC  >  USA300TCH1516_ALE/801807‑802095

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.