New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4024573	43 (0.760)	4 (0.070)	4/254	NT	8.7%	coding (249/489 nt)	rfaH	transcription antiterminator RfaH
	?	NC_000913	= 4024606	43 (0.790)					coding (216/489 nt)	rfaH	transcription antiterminator RfaH

GCCTGAAAGCCTTCGAACGCGCCTTCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTT  >  NC_000913/4024439‑4024715                                                                                                                                       |                                                                                                                                               cccTGAAGGCCGTCGAACGCGGCTTCGGTAATAATCACCTTATCACGCGGATAAGTGGTCGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCaaa                                                                                                                                        <  2:1017512/142‑1 (MQ=255)   cTGAAAGCCTTCGAGCGCGCCTTCGGTAATAATCACCTTGTCACCCGGATAGGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGATTATCGCTGGCGACGCGCCAAAgc                                                                                                                                      <  2:813747/143‑1 (MQ=255)    tGAAAGCCTTCGAACGCGCCTTCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGCTGGGACTATCGCTGGCGACGCGCCACAgcg                                                                                                                                     >  1:948004/1‑143 (MQ=255)      aaaGCCTTCGAACGCGCCTTCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCa                                                                                                                                   <  1:1010589/143‑1 (MQ=255)          ccTTTGATCGCGCCTTCGGTAATAATCACCTTATCCCCCGGATAAGGGGGTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGaa                                                                                                                               <  1:44132/143‑1 (MQ=255)            ttCGAACGCGCCTTCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGt                                                                                                                             >  2:821375/1‑143 (MQ=255)            ttCGAACGCGCCTTCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGt                                                                                                                             >  1:382662/1‑143 (MQ=255)             tCGAACGCGCCTTCGGTAATAATCACCTTATCACCCGGATAAGGGGATGCCGAAAGGTCACTGTTTTCAGGCCCAGAGCCCGATAGCTGATGAATAACCGCCAGTGGGGCTATCCGTGGCGACGCGCCGCAGCGCCCGAAggg                                                                                                                            >  2:132770/1‑141 (MQ=255)              cGAACGCGCCTTCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTgg                                                                                                                           <  1:101425/143‑1 (MQ=255)                   gcgcCTTCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATATCTTTGGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGAGCCAAAGCGCACGAAGTAGCTGac                                                                                                                      >  2:729797/1‑143 (MQ=255)                        ttCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGCAGTGGCTGACACcgc                                                                                                                 >  1:854146/1‑143 (MQ=255)                        ttCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCAAAAGCGAACGACGGGGCTGccacgcc                                                                                                                 >  1:1036960/1‑140 (MQ=255)                           ggTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGg                                                                                                              <  1:437790‑M2/143‑2 (MQ=255)                            gTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGgt                                                                                                             <  1:523785‑M2/143‑3 (MQ=255)                               ataatCGCCTTCTCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTTATGAATCACCGCCGATGGGACTATCGCTGGCGACccgcggtgtcagccacttcgtgcgctttggcgcgtcgc                                                                                                          <  2:508523‑M1/143‑39 (MQ=255)                               ataatCGCCTTATCACCCGGATAGGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGgtcgc                                                                                                          >  1:920269‑M2/1‑138 (MQ=255)                                 actCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGt                                                                                                        <  1:594487/141‑1 (MQ=255)                                 aatCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTCTCGATTTATACACCGATAGCGCATTAAGAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTAGCTGACACCGCGGGTCGCGt                                                                                                        <  1:567086/143‑1 (MQ=255)                                    cACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGa                                                                                                     <  2:880101/143‑1 (MQ=255)                                     aCCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCCCGCACCCCGCGCCGCGTTGAt                                                                                                    >  2:1066766/1‑143 (MQ=255)                                       cTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATGGGTGGCGTCGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTGGCGTTGATAg                                                                                                  >  1:41909/1‑143 (MQ=255)                                               ccGGATAAGCGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTa                                                                                          <  1:140761/143‑1 (MQ=255)                                                cgtaTACGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGACAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTTGCGTTGATAGTCGTGGTAt                                                                                         <  2:446635/140‑1 (MQ=255)                                                   aTAAGGTGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACccgcggtgtcagccacttcgtgcgctttggcgcgtcgccagcgatagtcccatcggcg                                                                                      <  1:367757‑M1/143‑59 (MQ=255)                                                        gggTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTAGGAATCACt                                                                                 >  2:1039795/1‑143 (MQ=255)                                                           ttGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGATGATAGGCGTGGTATGAATCACTTCt                                                                              >  1:17228/1‑143 (MQ=255)                                                                 gATCGACAATGTCTTTCGGTTTATATACTGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCa                                                                        <  1:38789/143‑1 (MQ=255)                                                                   tCGACAGTGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCaaa                                                                      <  1:283823/143‑1 (MQ=255)                                                                   tCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACccgcggtgtcagccacttcgtgcgctttggc                                                                                                                 <  2:983051‑M1/100‑32 (MQ=255)                                                                   tCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACccgcggtgtcagccacttcgtgcgctttggc                                                                                                                 >  1:983051‑M1/1‑69 (MQ=255)                                                                    cGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAAt                                                                     <  1:794617/143‑1 (MQ=255)                                                                       cAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTcc                                                                  <  1:821375/143‑1 (MQ=255)                                                                        aaTGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCca                                                                 <  2:437790/143‑1 (MQ=255)                                                                              tttCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACa                                                           >  2:36494/1‑143 (MQ=255)                                                                                  ggTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTa                                                       >  1:812679/1‑143 (MQ=255)                                                                                       atataCCGATAGCTGATGAGTAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACGCCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTgg                                                  <  1:1001259/143‑1 (MQ=255)                                                                                        tataCCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTggg                                                 <  1:1073094/143‑1 (MQ=255)                                                                                         ataCCGATAGCTGATGAATAACCGCCGATGGGAATATCGCTGGCGACGCGACAAAGAGCACGAAGTGGATGACACCGCGGGTGGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTgggg                                                >  1:723619/1‑143 (MQ=255)                                                                                          taCCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGa                                               <  1:639297/143‑1 (MQ=255)                                                                                          taCCGATAGCTGATGAATAACCGCCGATGAGACTATCGCTTGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGa                                               <  1:37515/143‑1 (MQ=255)                                                                                           aCCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGCAGTTGGGGaa                                              >  1:1078494/1‑143 (MQ=255)                                                                                                    tgatgaATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTCTGAATCACTTCTGGGTCAAATCCAACTGACACGTTGTTGGGGATCCATGCCTc                                     >  1:508767/1‑143 (MQ=255)                                                                                                    tgatgaATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTc                                     >  1:527521/1‑143 (MQ=255)                                                                                                     gatgaATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCa                                    <  2:523785/143‑1 (MQ=255)                                                                                                            acccgccgGTGGGACTATCGCGGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCactgactg                             <  2:475229/141‑1 (MQ=255)                                                                                                            aaCAGCCGATGGGGCTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGAGACCGCGGGGCGCGTTGGTAGGCGTGGGATGAATCACCTCTCGGTCAAATTCCACCAACAACTAGTTCGGGACAAATGGCTCacgaacgg                             >  2:320759/1‑137 (MQ=255)                                                                                                               cgccgATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGgtcgccagcgatagtcccatcggcggttattcatcagctatcggtatataaaccgaaagacattgtcgatccggcaacaccttat                          <  1:367757‑M2/143‑86 (MQ=255)                                                                                                                gccgATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGt                         >  2:688334/1‑143 (MQ=255)                                                                                                                          cTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCca               <  1:820463/143‑1 (MQ=255)                                                                                                                           tagcGCTGTCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCcac              <  2:1036960/140‑1 (MQ=255)                                                                                                                               gCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCaacgcac          >  2:202871/1‑143 (MQ=255)                                                                                                                                   gCGACccgcggtgtcagccacttcgtgcgctttggcgcgtcgccagcgatagtcccatcggcggttattcatcagctatcggtatataaaccgaaagacattgtcgatccggcaaccccctatccgggtgataaggcgattat      >  1:920269‑M1/1‑5 (MQ=255)                                                                                                                                   gCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGgtcgccagcgatagtcccatcggcggtgattcataagctatcggtatataaaccgaaagacattgtcgatccggcaaccccttatccgggtgagaaggcgattat      <  2:508523‑M2/143‑106 (MQ=255)                                                                                                                                     gACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGAtttt    <  1:1024032/143‑1 (MQ=255)                                                                                                                                     gACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGAtttt    >  2:994510/1‑143 (MQ=255)                                                                                                                                      aCccgcggtgtcagccacttcgtgcgctttggcgcgtcgccagcgatagtcccatcggcggttattcatcagctatcggtatataaaccgaaagacattgtcgatccggcaaccccttatccgggtgataaggtgattattac   <  1:523785‑M1/143‑142 (MQ=255)                                                                                                                                      aCGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGAttttt   <  1:891304/143‑1 (MQ=255)                                                                                                                                       cccgcggtgtcagccacttcgtgcgctttggcgcgtcgccagcgatagtcccatcggcggttattcatcagctatcggtatataaaccgaaagacattgtcgatccggcaaccccttatccgggtgataaggtgattattacc  <  1:437790‑M1/143‑143 (MQ=255)                                                                                                                                       |                                                                                                                                               GCCTGAAAGCCTTCGAACGCGCCTTCGGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTT  >  NC_000913/4024439‑4024715

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.