New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4963796 =	43 (0.990)	3 (0.070)	3/240	NT	6.7%	intergenic (‑97/+131)	fleS/fleQ	two‑component system sensor histidine kinase FleS/transcriptional regulator FleQ
	?	NC_002947	4963899 =	43 (1.050)					intergenic (‑200/+28)	fleS/fleQ	two‑component system sensor histidine kinase FleS/transcriptional regulator FleQ

GTAGCAATAGCCGTGCCGGAGATGGGGGTTTGGGTTTGACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCCGCGCGCGCAACGATACCGTTGGC  >  NC_002947/4963750‑4964046                                                                                                                                                      |                                                                                                                                                     gaccaggcggaggattgatgtttgggctgggtgttcgccttgggggTTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAAc                                                                                                                                                      >  2:188543‑M1/47‑150 (MQ=255)  accaggcggaggattgatgtttgggctgggtgttcgccttgggggTTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAAcc                                                                                                                                                     >  1:969309‑M1/46‑150 (MQ=255)               gCCGGAGATGGGGGTTTGGGTTTGACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAaca                                                                                                                                        <  2:167020/150‑1 (MQ=255)                         ggggTTTGGGTTTGACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCaa                                                                                                                             >  1:489756/1‑150 (MQ=255)                                  gtttgACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAAtc                                                                                                                    <  1:288999/150‑1 (MQ=255)                                            ggATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTgg                                                                                                          <  2:489756/150‑1 (MQ=255)                                             ggttgcgtttgggcggggtgttcgccttgaggtttttgtttgggcggcgctcgatctccgcggcacaacaaaactcacggcgaacccttctcggtcttaacgcaaCCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGt                                                                                                         >  1:969309‑M2/106‑150 (MQ=255)                                             gATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGt                                                                                                         >  2:840664/1‑150 (MQ=255)                                              gttgcgtttgggcggggtgttcgccttgaggtttttgtttgggcggcgctcgatctccgcggcacaacaaaactcacggcgaacccttctcggtcttaacgcaaCCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTc                                                                                                        >  2:188543‑M2/105‑150 (MQ=255)                                              aTTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTc                                                                                                        <  2:764946/150‑1 (MQ=255)                                                   GTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCAc                                                                                                   <  1:321708‑M1/150‑1 (MQ=255)                                                   GTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCAc                                                                                                   <  2:117041‑M1/150‑1 (MQ=255)                                                           cGAGAAGGGTTCGCCGTGAGTTGTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGCATACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTgg                                                                                           <  1:447768/150‑1 (MQ=255)                                                             agaAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCGAAGAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTggcg                                                                                         >  2:490060/1‑150 (MQ=255)                                                                    ttCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATg                                                                                  >  1:913464/1‑150 (MQ=255)                                                                        ccGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCCATATTCCTCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGt                                                                              >  1:607952/1‑150 (MQ=255)                                                                         cGTGAGTTTTGTTGTGCCGAGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTa                                                                             >  1:1037702/1‑150 (MQ=255)                                                                           tGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAAtcctcc                                                                                                                >  2:1014239/1‑113 (MQ=255)                                                                           tGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAAtcctcc                                                                                                                <  1:1014239/113‑1 (MQ=255)                                                                           tGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACt                                                                           >  2:490693/1‑150 (MQ=255)                                                                               ttttGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTgcg                                                                       >  1:460973/1‑150 (MQ=255)                                                                                    ttgtGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCAttt                                                                  >  2:1113619/1‑150 (MQ=255)                                                                                        gcggcgctcgatctccgcggcacaacaaaactcacggcgaacccttctcggtcttaacgcaaCCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTtctc                                                              <  1:188543‑M2/88‑1 (MQ=255)                                                                                        gCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTtctc                                                              <  1:117041/150‑1 (MQ=255)                                                                                         ctgcgGATATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCg                                                             >  2:1035320/3‑150 (MQ=255)                                                                                         ccGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCg                                                             >  2:837373/1‑150 (MQ=255)                                                                                           gcgGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGAc                                                           >  1:885142/1‑150 (MQ=255)                                                                                           gcgGAGATCGAGCGCCACCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGAc                                                           >  1:367063/1‑150 (MQ=255)                                                                                            cgGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGAcc                                                          >  1:457100/1‑150 (MQ=255)                                                                                               agaTCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGCCCAgg                                                       <  2:885142/150‑1 (MQ=255)                                                                                               agaTCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAgg                                                       <  2:93964/150‑1 (MQ=255)                                                                                               agaTCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAgg                                                       <  2:179763/150‑1 (MQ=255)                                                                                                gaTCGAGCGCCGCCCAAACAAAACTCTCATGGCGAACGCCCCGCCCAAAAG‑AACCAAAATATCCTCCGGTATGCCCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAggg                                                      <  1:570142/150‑1 (MQ=255)                                                                                                    gAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGggtggt                                                  >  2:203747/1‑150 (MQ=255)                                                                                                               aaacaaaAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTgg                                                                                           <  2:681353/98‑1 (MQ=255)                                                                                                               aaacaaaAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTgg                                                                                           >  1:681353/1‑98 (MQ=255)                                                                                                               aaacaaaAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATAc                                       <  1:837373/150‑1 (MQ=255)                                                                                                                   aaaaaCCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATAccgca                                   >  2:609278/1‑146 (MQ=255)                                                                                                                         cTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTc                             >  2:78931/1‑150 (MQ=255)                                                                                                                          tCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTggc                                                                                          >  2:267690/1‑88 (MQ=255)                                                                                                                          tCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTggc                                                                                          <  1:267690/88‑1 (MQ=255)                                                                                                                          tCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCa                            >  2:399739/1‑150 (MQ=255)                                                                                                                          tCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCa                            >  2:589861/1‑150 (MQ=255)                                                                                                                            aaGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGc                          <  2:276317/150‑1 (MQ=255)                                                                                                                            aaGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGc                          >  1:276317/1‑150 (MQ=255)                                                                                                                             aGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGcc                         >  1:184930/1‑150 (MQ=255)                                                                                                                              ggCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCcg                        >  2:40650/1‑150 (MQ=255)                                                                                                                                 gAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCcgcgc                     <  1:490060/150‑1 (MQ=255)                                                                                                                                  aaCACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCcgcgcg                    >  2:44759/1‑150 (MQ=255)                                                                                                                                        ccGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCACCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCCGCGCGCGCAAc              <  2:755344/150‑1 (MQ=255)                                                                                                                                             cAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCCGCGCGCGCAACGATAc         <  1:1035320/150‑1 (MQ=255)                                                                                                                                                 cgcaaCCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCCGCGCGCGCAACGATACCGtt     <  2:1083902‑M2/145‑1 (MQ=255)                                                                                                                                                   caaCCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCCGCGCGCGCAACGATACCGTTgg   <  2:1037702‑M2/147‑1 (MQ=255)                                                                                                                                                    aaCCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCCGCGCGCGCAACGATACCGTTGGc  >  2:750015‑M2/3‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                     GTAGCAATAGCCGTGCCGGAGATGGGGGTTTGGGTTTGACGTAGGATTGCGTTAAGACCGAGAAGGGTTCGCCGTGAGTTTTGTTGTGCCGCGGAGATCGAGCGCCGCCCAAACAAAAACCTCAAGGCGAACACCCCGCCCAAACGCAACCCCCAAGGCGAACACCCAG‑CCCAAACATCAATCCTCCGCCTGGTCCTCACCGCCCTGGCGGCTCATGCCGTACTTGCGCATTTTCTCGACCAGGGTGGTACGGCGAATACGCAAACGTTCAGCCGCGCGCGCAACGATACCGTTGGC  >  NC_002947/4963750‑4964046

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.