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

GGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCAGGGTGATCATCGGTGCCAGGCAATT  >  NC_000913/4024465‑4024743                                                                                                                                              |                                                                                                                                          ggTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGg                                                                                                                                          <  1:437790‑M2/143‑2 (MQ=255)  gTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGgt                                                                                                                                         <  1:523785‑M2/143‑3 (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)                              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)                                          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)                                                                                                         gCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGgtcgccagcgatagtcccatcggcggtgattcataagctatcggtatataaaccgaaagacattgtcgatccggcaaccccttatccgggtgagaaggcgattat                                  <  2:508523‑M2/143‑106 (MQ=255)                                                                                                           gACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGAtttt                                >  2:994510/1‑143 (MQ=255)                                                                                                           gACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGAtttt                                <  1:1024032/143‑1 (MQ=255)                                                                                                            aCGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGAttttt                               <  1:891304/143‑1 (MQ=255)                                                                                                                gcCAAGGCGCATGAAGGGGCTGACACCGCGGGTCGCGTTGATGGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCa                           <  2:854146/143‑1 (MQ=255)                                                                                                                gcCAAAGCGCACGAAGTGGCTGACACCGCGGgtcgccagcgatagtcccatcggcggttattcatcagctatcggtatataaaccgaaagacattgtcga                                                                      >  1:983051‑M2/1‑31 (MQ=255)                                                                                                                gcCAAAGCGCACGAAGTGGCTGACACCGCGGgtcgccagcgatagtcccatcggcggttattcatcagctatcggtatataaaccgaaagacattgtcga                                                                      <  2:983051‑M2/100‑70 (MQ=255)                                                                                                                  cAAAGCGCACGAAGTGGCTCACCCCGCGGTTCGCGTTTATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCAgg                         <  1:226911/143‑1 (MQ=255)                                                                                                                   aaaGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCGCAAACAGGTAGTTGGGGGACCATGGCTCACTGGCTGCAGTACGGGTTCCACGCACGCTTGTTTCCAggg                        >  1:1008315/1‑143 (MQ=255)                                                                                                                     aGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCAGGGTg                      >  2:40132/1‑143 (MQ=255)                                                                                                                             aaGTGGTTGGCGCCGCGGGCCGTGTGGGGAGTGGTGGGATGAATCACCTCTGGGTCAAATGCCACAAACAGGTGGTTGGGGAACAAGGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCAGGGTGATCATCgg              <  2:1008533/143‑1 (MQ=255)                                                                                                                              acaggCTGACACCGGGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGGAGTTGGGGAACAATGGCTCCCTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCAGGGTGATCATCGGt             <  1:285783/140‑1 (MQ=255)                                                                                                                              aGTGGCTGACACCGCGGGTCGCTTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGTAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCAGGGTGATCATCGGt             <  1:286810/143‑1 (MQ=255)                                                                                                                                  gCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCAGGGTGATCATCGGTGCCa         >  1:825272/1‑143 (MQ=255)                                                                                                                                    tGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCAGGGTGATCATCGGTGCCAgg       <  1:837514/143‑1 (MQ=255)                                                                                                                                    tGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTATGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGGTGTTTTCCAGGGTGGTCATCGGTGCCAgg       >  1:211066/1‑143 (MQ=255)                                                                                                                                       cacCGCGGGTCGCGTTGATAGGCGTGGTATGAATCACTGCTGGGTCAGATTCCACAAACAGGTAGTTGGGGAACAAGGGCTCACTGACTGCAGTACGTTTGCCACGCACGATTTTTGCCAGGGTGATCATCGGTGCCAGGCaa    <  2:1078494/143‑1 (MQ=255)                                                                                                                                         ccGCGGGTCGCGTTGATAGTCGTGGTATGAAGCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGCTTTTTTCCGGGGTGATCATCGTTGCCCGGCAttt  >  2:395989/1‑143 (MQ=255)                                                                                                                                              |                                                                                                                                          GGTAATAATCACCTTATCACCCGGATAAGGGGTTGCCGGATCGACAATGTCTTTCGGTTTATATACCGATAGCTGATGAATAACCGCCGATGGGACTATCGCTGGCGACGCGCCAAAGCGCACGAAGTGGCTGACACCGCGGGTCGCGTTGATAGTCGTGGTATGAATCACTTCTGGGTCAAATTCCACAAACAGGTAGTTGGGGAACAATGGCTCACTGACTGCAGTACGTTTTCCACGCACGATTTTTTCCAGGGTGATCATCGGTGCCAGGCAATT  >  NC_000913/4024465‑4024743

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.