New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	3478133 =	46 (0.880)	3 (0.060)	3/234	NT	6.5%	coding (514/543 nt)	PP_3089	hypothetical protein
	?	NC_002947	3478187 =	42 (0.840)					coding (460/543 nt)	PP_3089	hypothetical protein

AGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGCTGACCGCCTTGTCTTCACCACTCTGGTT  >  NC_002947/3477984‑3478271                                                                                                                                                      |                                                                                                                                           acaggctaTTGAGAATCTCAGGCATAGCACTCTGTGGACATGGCTAGTGAACAGCGCGGCGGAGGGCCCGGCGCGCCGCGGAACAGCGGCCGCCGAAGCGGCCCATGGTGCGGTGCGTGCTGAGGGAAACACTGTGGTCGCGGTGCGGTc                                                                                                                                            <  2:111163/143‑1 (MQ=255)        aTTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGcca                                                                                                                                     >  1:382048/1‑150 (MQ=255)                   cAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGtt                                                                                                                          <  2:382048/150‑1 (MQ=255)                         tAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTgccgcc                                                                                                                    >  1:655645/1‑150 (MQ=255)                          aGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGccgccg                                                                                                                   <  1:693221/150‑1 (MQ=255)                              cacTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCt                                                                                                               >  1:459018/1‑150 (MQ=255)                                  ctGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGtt                                                                                                                          <  2:1225661/135‑1 (MQ=255)                                  ctGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGtt                                                                                                                          >  1:1225661/1‑135 (MQ=255)                                   tGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCg                                                                                                          >  1:1209055/1‑150 (MQ=255)                                     gACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTc                                                                                                        <  1:563575/150‑1 (MQ=255)                                        aTGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGt                                                                                                     >  2:354242/1‑150 (MQ=255)                                           gCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCg                                                                                                  >  2:1208683/1‑150 (MQ=255)                                                tGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTct                                                                                             <  2:1209055/150‑1 (MQ=255)                                                  aaCAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTctgc                                                                                           >  1:1195408/1‑150 (MQ=255)                                                    cAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTctgctg                                                                                         <  2:129267/150‑1 (MQ=255)                                                     aGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTgg                                                                                        <  1:417062/150‑1 (MQ=255)                                                          gcCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAAAACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTa                                                                                   >  1:1219871/1‑150 (MQ=255)                                                           ccGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAg                                                                                  <  2:640648/150‑1 (MQ=255)                                                               aaaaCCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAggtgg                                                                              <  2:692351/150‑1 (MQ=255)                                                                          cgcTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCgg                                                                   <  2:459018/150‑1 (MQ=255)                                                                          cgcTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCgg                                                                   <  1:354242/150‑1 (MQ=255)                                                                             tGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTgg                                                                                        <  1:216963/126‑1 (MQ=255)                                                                             tGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTgg                                                                                        >  2:216963/1‑126 (MQ=255)                                                                                  aaCACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGCCGGTGGTCTTTATGCGGGCAAAGtt                                                           <  2:1195408/150‑1 (MQ=255)                                                                                      caGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGAAAGGTAGaat                                                       <  2:355226/150‑2 (MQ=255)                                                                                             ccgAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGAttt                                                >  2:93337/1‑150 (MQ=255)                                                                                                aaGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATttctt                                             <  1:1208683/150‑1 (MQ=255)                                                                                                aaGCGGCCCATGGTTCGGTACGTGCGTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATttctt                                             <  2:655645/150‑1 (MQ=255)                                                                                                      cccATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTg                                                                                                              >  1:793143/1‑79 (MQ=255)                                                                                                      cccATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTg                                                                                                              <  2:793143/79‑1 (MQ=255)                                                                                                            gTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGt                                 >  1:651704/1‑150 (MQ=255)                                                                                                             ttCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTc                                >  1:901796/1‑150 (MQ=255)                                                                                                                       ttcaactttgcccgcatcaagaccacctacaCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGCTGACCGcc                      <  2:1293494‑M1/119‑1 (MQ=255)                                                                                                                       gCTTAGGCAAACACTTTGTTCGTGGTGCGGTCACAGCGACCCACGATGTTGTCGTCGGCCTGGCAGTCAGTGCGGTTCTGCTGGGTGTTGGTGGTCTTGTCGCGAGAAAAGTTGAAGGTGATTTATTCAACGGCGAGGTGGCTGACCggc                      >  2:425977/1‑148 (MQ=255)                                                                                                                           aGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCgg                                                                   >  2:900165/1‑101 (MQ=255)                                                                                                                           aGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCgg                                                                   <  1:900165/101‑1 (MQ=255)                                                                                                                            ctttgcccgcatcaagaccacctacaCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTgg                                                                                        <  1:945722‑M1/53‑1 (MQ=255)                                                                                                                            ctttgcccgcatcaagaccacctacaCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTgg                                                                                        >  2:945722‑M1/27‑79 (MQ=255)                                                                                                                             gCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGtt                                                                                               <  2:1081905/71‑1 (MQ=255)                                                                                                                             gCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGtt                                                                                               >  1:1081905/1‑71 (MQ=255)                                                                                                                               aaaCACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAGAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGCTGACCGCCTTGTCTTc              >  1:1246379/1‑150 (MQ=255)                                                                                                                               aaaCACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGCTGACCGCCTTGTCTTc              <  2:881745/150‑1 (MQ=255)                                                                                                                               aaaCACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGCTGACCGCCTTGTCTTc              >  1:413264/1‑150 (MQ=255)                                                                                                                                   acTTTGTTTGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGGCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGGTGAAGCTGATTTCTTCTTCGGGCAGGTCGCTGACCGCCATGTCTTcacca          <  2:851642/150‑1 (MQ=255)                                                                                                                                   acTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATttctt                                             <  2:588396/115‑1 (MQ=255)                                                                                                                                   acTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATttctt                                             >  1:588396/1‑115 (MQ=255)                                                                                                                                    cTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGCTGACCGCCTTGTCTTcaccac         >  1:588679/1‑150 (MQ=255)                                                                                                                                     tttGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGAt                                                                       >  1:993559/1‑87 (MQ=255)                                                                                                                                     tttGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGAt                                                                       <  2:993559/87‑1 (MQ=255)                                                                                                                                           cgcgGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGCTGACCGCCTTGTCTTCACCACTCTGGtt  <  2:1246379/150‑1 (MQ=255)                                                                                                                                                  cggtCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTgg                                                                                        <  2:186031/57‑1 (MQ=255)                                                                                                                                                  cggtCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTgg                                                                                        >  1:186031/1‑57 (MQ=255)                                                                                                                                                     tCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGc                              >  1:1201835/1‑112 (MQ=255)                                                                                                                                                     tCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGc                              <  2:1201835/112‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                           AGAGGTCATTGAGAATTTCAGGCATAGAACACTCTGGACATGGCTAGTGAACAGCGCGCCGGAAAACCCGGCGCGCTGCGGAACACAGGCCGCCGAAGCGGCCCATGGTTCGGTACGTGCTTAGGCAAACACTTTGTTCGCGGTGCGGTCCCAGCCACCCACGATGTTGCCGCCGGCCTGGCCGTCGGTGCGGTTCTGCTGGGTGTAGGTGGTCTTGATGCGGGCAAAGTTGAAGCTGATTTCTTCAACGGGCAGGTCGCTGACCGCCTTGTCTTCACCACTCTGGTT  >  NC_002947/3477984‑3478271

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