New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2207748 =	59 (1.280)	3 (0.070)	3/238	NT	5.6%	intergenic (+109/+155)	rodA/USA300HOU_RS11255	Peptidoglycan glycosyltransferase RodA/hypothetical protein
	?	USA300TCH1516_ALE	2207798 =	47 (1.110)					intergenic (+159/+105)	rodA/USA300HOU_RS11255	Peptidoglycan glycosyltransferase RodA/hypothetical protein

TCAAATATCATAACTTTTCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATTAGATGCTGG  >  USA300TCH1516_ALE/2207658‑2207938                                                                                                                                             |                                                                                                                                             tCAAATATCATAACTTTTCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGAttt                                                                                                                                              >  1:716124/1‑141 (MQ=255)  cAAATATCATAACTTTTCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGAtttt                                                                                                                                             <  2:262437/141‑1 (MQ=255)   tcacacaccgttaaagctatcgtcggactattcgatgatagcttttttgactggatttactaaaatgaaagcaagtactatataacaa‑‑TCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGtt                                                                                                                                          >  2:268478‑M1/89‑141 (MQ=255)    aaTATCATAACTTTTCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGt                                                                                                                                           <  2:291824/141‑1 (MQ=255)        tCATAACTTTTCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTtata                                                                                                                                       >  1:395501/1‑141 (MQ=255)         cATAACTTTTCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATAGAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTtatat                                                                                                                                      <  1:50641/141‑1 (MQ=255)             aCTTTTCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTa                                                                                                                                  <  2:163661/141‑1 (MQ=255)               ttttCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACt                                                                                                                                <  1:457423/141‑1 (MQ=255)               ttttCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACt                                                                                                                                <  1:521265/141‑1 (MQ=255)               ttttCAAGATGACGTTATATAGTCTAGTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACt                                                                                                                                <  2:201987/141‑1 (MQ=255)                 ttCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTg                                                                                                                              <  1:100946/141‑1 (MQ=255)                   cAAGATGACGTTATATNGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCt                                                                                                                            >  1:635430/1‑141 (MQ=255)                   cAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCt                                                                                                                            >  1:349764/1‑141 (MQ=255)                   cAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCt                                                                                                                            <  2:173482/141‑1 (MQ=255)                   cAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCt                                                                                                                            >  2:46145/1‑141 (MQ=255)                        tGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCAt                                                                                                                       >  2:266222/1‑141 (MQ=255)                           cGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCAtttt                                                                                                                    <  1:37919/141‑1 (MQ=255)                             ttATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAg                                                                                                                  >  2:87603/1‑141 (MQ=255)                                 ataGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTaaa                                                                                                              <  1:687769/141‑1 (MQ=255)                                      cTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAg                                                                                                         <  1:87921/141‑1 (MQ=255)                                      cTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAg                                                                                                         <  1:349012/141‑1 (MQ=255)                                      cTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAg                                                                                                         >  1:61010/1‑141 (MQ=255)                                        aTTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTc                                                                                                       >  1:716423/1‑141 (MQ=255)                                              gtcgtcGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCaaaaaa                                                                                                 >  1:419320/1‑141 (MQ=255)                                                cgtcgATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAGACCAGTCAAAAAAGc                                                                                               >  1:242157/1‑141 (MQ=255)                                                  tcgATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTa                                                                                             >  1:46384/1‑141 (MQ=255)                                                    gATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTatc                                                                                           >  2:3859/1‑141 (MQ=255)                                                      tttAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTatcat                                                                                         <  2:10026/141‑1 (MQ=255)                                                            aTGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATa                                                                                   >  2:251590/1‑141 (MQ=255)                                                             tGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAg                                                                                  <  2:15353/141‑1 (MQ=255)                                                               tCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTc                                                                                <  1:649322/141‑1 (MQ=255)                                                               tCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTc                                                                                >  1:165545/1‑141 (MQ=255)                                                                 atatatAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCcg                                                                              <  1:239154/141‑1 (MQ=255)                                                                   atataGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCcgac                                                                            >  1:637012/1‑141 (MQ=255)                                                                    tataGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCcgacg                                                                           >  1:514326/1‑141 (MQ=255)                                                                     ataGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCcgacga                                                                          <  1:192535/141‑1 (MQ=255)                                                                           atTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCtt                                                                    <  1:138922/141‑1 (MQ=255)                                                                           atTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCtt                                                                    <  2:14619/141‑1 (MQ=255)                                                                                 cGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACgg                                                              >  1:391370/1‑141 (MQ=255)                                                                                   ataataACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGgtg                                                            >  2:39161/1‑141 (MQ=255)                                                                                    taataaCAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGgtgt                                                           >  1:286789/1‑141 (MQ=255)                                                                                    taataaCAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGgtgt                                                           <  1:726175/141‑1 (MQ=255)                                                                                        aacaaaatccctctttagagtgtacattttacaatgtgtacttcaaagagggaTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGa                                                       >  2:268478‑M2/54‑141 (MQ=255)                                                                                         aCAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGAt                                                      >  2:186732/1‑141 (MQ=255)                                                                                         aCAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGAt                                                      >  2:165547/1‑141 (MQ=255)                                                                                         aCAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGAt                                                      >  1:477880/1‑141 (MQ=255)                                                                                           AATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTc                                                    <  1:670527‑M1/141‑1 (MQ=255)                                                                                            ATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTca                                                   <  2:46852‑M1/141‑1 (MQ=255)                                                                                                ctctttagagtgtacattttacaatgtgtacttcaaagagggattTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAAt                                               >  1:125560‑M2/46‑141 (MQ=255)                                                                                                 tctttagagtgtacattttacaatgtgtacttcaaagagggattTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATc                                              >  1:72093‑M2/45‑141 (MQ=255)                                                                                                 TCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATc                                              <  1:289266‑M1/141‑1 (MQ=255)                                                                                                         gTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCaa                                      >  1:11345/1‑141 (MQ=255)                                                                                                          gatctaTTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAat                                     <  1:724950/136‑1 (MQ=255)                                                                                                                 tGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTa                              >  1:532526/1‑141 (MQ=255)                                                                                                                     aaaTGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTc                          >  1:300960/1‑141 (MQ=255)                                                                                                                        tGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTg                       >  1:46443/1‑141 (MQ=255)                                                                                                                           acacTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGact                    <  1:720269/141‑1 (MQ=255)                                                                                                                              ctctAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGacttac                 <  2:10861/141‑1 (MQ=255)                                                                                                                                    agagggattTTGTTATATAGTACTTGCTTTCATTTTAGTTAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTttatt           <  1:605959‑M2/132‑1 (MQ=255)                                                                                                                                           ttTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATTAGATGCt    >  1:712698‑M2/3‑141 (MQ=255)                                                                                                                                            tTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATTAGATGCTg   <  1:183663‑M2/140‑1 (MQ=255)                                                                                                                                             ttGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATTAGATGCTgg  <  2:163125/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                             TCAAATATCATAACTTTTCAAGATGACGTTATATAGTCTATTTACGTCGTCGATTTAAAATGTCATATATAGATATTACTCGATAATAACAATCCCTCTTTGAAGTACACATTGTAAAATGTACACTCTAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATTAGATGCTGG  >  USA300TCH1516_ALE/2207658‑2207938

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.