New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4536203 =	NA (NA)	5 (0.080)	5/258	NT	12.5%	intergenic (+730/‑85)	PP_4022/PP_4024	hypothetical protein/transposase
	?	NC_002947	4944914 =	35 (0.590)					intergenic (+274/+524)	PP_5673/flhB	D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein

CGGGGCGTTCTGGACGGTCAGTACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGTGGACTTTCG  >  NC_002947/4536058‑4536349                                                                                                                                                  |                                                                                                                                                   cGGGGAGTTCTGGACGGTCAGTACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTaa                                                                                                                                                 <  6:259500/149‑1 (MQ=255)    ggCGTTCTGGACGGTCAGTACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAgg                                                                                                                                               >  4:248001/1‑148 (MQ=255)      cGTTCTGGACGGTCAGTACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGAt                                                                                                                                            <  3:297791/149‑1 (MQ=255)        ttCTGGACGGTCAGTACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATTTACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGTGCAGGTGGACTATATCGTTGTAAGGGATcc                                                                                                                                          <  5:133735/149‑1 (MQ=255)        ttCTGGACGGTCAGTACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATcc                                                                                                                                          <  3:190578/149‑1 (MQ=255)             gACGGTCAGTACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGTTCcatc                                                                                                                                       <  5:63764/147‑1 (MQ=255)                  tCAGTACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTGTATCGTTGTAAGGGATCCATCATCCCca                                                                                                                                >  3:349236/1‑149 (MQ=255)                      tACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACAtt                                                                                                                            >  8:196010/1‑149 (MQ=255)                             ctgctgTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAAcc                                                                                                                      <  8:322274/148‑1 (MQ=255)                                ctgTAGCCCTTCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGGATGAACTTCGTCAGGTACATCGCGGCGGTGACGGTTTTCATCATTTGCGGGGAGGTGGACTATATCGTTGTAAGGGATCca                                                                                                                                         <  6:123230/126‑1 (MQ=255)                                ctgTACCCCATCGACCTGGTACGCCCCACCGGCGTCGCGCGCACCAAGAACATCGTCAGCAACATCGCGGCGCAGACCCTTATCAACATTTCCCGGCACGTGGACTATATCGATCTAACGCATCca                                                                                                                                         >  5:123230/1‑126 (MQ=255)                                    aCCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCt                                                                                                              >  1:254341/1‑149 (MQ=255)                                      cccATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCca                                                                                                                                         <  6:194169/120‑1 (MQ=255)                                      cccATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCca                                                                                                                                         >  5:194169/1‑120 (MQ=255)                                        cATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCcatc                                                                                                                                       >  8:229897/1‑120 (MQ=255)                                        cATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCcatc                                                                                                                                       <  7:229897/120‑1 (MQ=255)                                             aCCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTcc                                                                                                                  >  8:29861/1‑136 (MQ=255)                                             aCCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTcc                                                                                                                  <  7:29861/136‑1 (MQ=255)                                              ccTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGAt                                                                                                    >  2:75334/1‑149 (MQ=255)                                                tGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTc                                                                                                                   <  4:39422/132‑1 (MQ=255)                                                     cgcgCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCtgtg                                                                                              <  2:292639/148‑1 (MQ=255)                                                          cAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCg                                                                                        <  7:196010/149‑1 (MQ=255)                                                                 gTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGAtttctt                                                                                 <  3:248001/149‑1 (MQ=255)                                                                 gTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGAtttctt                                                                                 >  5:273483/1‑149 (MQ=255)                                                                            caTGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGagccag                                                                      <  1:75334/149‑1 (MQ=255)                                                                                 aCTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGc                                                                 >  4:252028/1‑149 (MQ=255)                                                                                      gTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTGTATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCatg                                                             <  4:349236/148‑1 (MQ=255)                                                                                           cAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATg                                                                                                   <  4:108961/105‑1 (MQ=255)                                                                                           cAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATg                                                                                                   >  3:108961/1‑105 (MQ=255)                                                                                             aCATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGccc                                                     <  6:273483/149‑1 (MQ=255)                                                                                                tCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGa                                                  >  5:239322/1‑149 (MQ=255)                                                                                                                 ttCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAg                                 >  8:188150/1‑149 (MQ=255)                                                                                                                   catcatTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTTCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGtc                               >  6:302/1‑149 (MQ=255)                                                                                                                   catcatTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGtc                               >  1:360000/1‑149 (MQ=255)                                                                                                                    atcatTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCAAAATCCAACCGTCCACCTGATTCCCGATGATGTGCTCCCGATTTCTTTCTGGAGCCAGCCCTCCATGATGCGCCCCGACAGCAAAGTAGAAAAAGtc                               >  5:20803/1‑148 (MQ=17)                                                                                                                     tcatTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGcccc                                                    <  2:75723/126‑1 (MQ=255)                                                                                                                     tcatTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGcccc                                                    >  1:75723/1‑126 (MQ=255)                                                                                                                     tcatTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGtctc                             >  6:241450/1‑148 (MQ=255)                                                                                                                     tcatTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGtcta                             >  6:204148/1‑149 (MQ=255)                                                                                                                      catTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCaaa                                           >  7:339194/1‑134 (MQ=255)                                                                                                                      catTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCaaa                                           <  8:339194/134‑1 (MQ=255)                                                                                                                      catTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGtctac                            >  8:18550/1‑149 (MQ=255)                                                                                                                         ttCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGtctacctc                         >  6:45408/1‑149 (MQ=255)                                                                                                                         ttCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGtctacct                          >  8:8129/1‑148 (MQ=255)                                                                                                                              ggCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCtgt                                                                                               >  2:127935/1‑74 (MQ=255)                                                                                                                              ggCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCtgt                                                                                               <  1:127935/74‑1 (MQ=255)                                                                                                                                     ggACTATATCGTAGTAAGGGATCCATAATCACCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTACCGATTTCTTTATGGAGCCAGCCCGCCAAGATGCGCACCGACAGCAAAGACGAAAAAGTCTACCTCTACCCCAAGccc             >  3:50075/1‑149 (MQ=11)                                                                                                                                       aCTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGt           >  5:83898/1‑149 (MQ=38)                                                                                                                                       aCTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGt           >  3:300581/1‑149 (MQ=38)                                                                                                                                        cTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGTg          >  5:277952/1‑149 (MQ=37)                                                                                                                                        cTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGTg          <  3:230758/149‑1 (MQ=37)                                                                                                                                           tatCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGTGGAc       >  2:151226/1‑149 (MQ=34)                                                                                                                                           tatCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAACTCTACCTCTACCCCAAGCCCGTGGAc       >  1:16512/1‑149 (MQ=21)                                                                                                                                               gTTGTATGGGATCCATCATCGCCACATTCCAACCGTCGAGCTGATTCCCGATGCTGTGCTGCCGATTTCTTTGTGGAGCCAGCCCGCCATGATGCGCCCCGACTGCTAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGTGGTCttt    <  2:16512/148‑1 (MQ=11)                                                                                                                                               gTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGTGGACttt    <  3:252028/148‑1 (MQ=31)                                                                                                                                                ttGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGTGGACTTTCg  <  6:239322/149‑1 (MQ=11)                                                                                                                                                ttGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGTGGACTTTCg  <  5:204148/149‑1 (MQ=11)                                                                                                                                                  |                                                                                                                                                   CGGGGCGTTCTGGACGGTCAGTACCCTGCTGCTGTACCCCATCGACCTGGTACGCGCCAGCGGCGTGGCGCGCAGCATGAACTTCGTCAGCAACATCGCGGCGCTGACGGTTTTCATCATTTCCGGGCAGGTGGACTATATCGTTGTAAGGGATCCATCATCCCCACATTCCAACCGTCCACCTGATTCCCGATGCTGTGCTCCCGATTTCTTTCTGGAGCCAGCCCGCCATGATGCGCCCCGACAGCAAAGTCGAAAAAGTCTACCTCTACCCCAAGCCCGTGGACTTTCG  >  NC_002947/4536058‑4536349

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.