New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1962621	22 (0.440)	23 (0.470)	16/284	2.7	51.1%	coding (352/393 nt)	flhE	proton seal during flagellar secretion
	?	NC_000913	2101749 =	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region

TTCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAT  >  NC_000913/2101609‑2101885                                                                                                                                             |                                                                                                                                         ttCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTAGTTGTAGTaagga                                                                                                                                        >  2:350694/1‑143 (MQ=255) ttCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGGACCAGCGTAACTGATCCTGCGCACCAATCAACAACAGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTaagga                                                                                                                                        >  1:495178/1‑143 (MQ=255)  tCACAGTACATAAAGGAACCTTGAGCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTaaggaa                                                                                                                                       <  2:144157/143‑1 (MQ=255)     caGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGt                                                                                                                                    <  1:262645/143‑1 (MQ=255)       gTACAGAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGTTACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGc                                                                                                                                  <  2:260487/143‑1 (MQ=255)           aTAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAAt                                                                                                                              >  1:575622/1‑143 (MQ=255)               tgTAACTTTGATCTAAGTCATTTACACGTACAAAATGTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGc                                                                                                                          <  1:166399/142‑1 (MQ=255)                 tAACCTGGAGCGAAGCCATTTACACGCACGAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTGTTGTTTTATTAAGGAAGGTGCGAATAAGCgg                                                                                                                        <  2:115417/143‑1 (MQ=255)                     cTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGaa                                                                                                                    >  1:732110/1‑143 (MQ=255)                     cTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGaa                                                                                                                    >  1:770220/1‑143 (MQ=255)                      ttGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGCTTTATTAAGGAAGGTGCGAATAAGCGGGGaaa                                                                                                                   >  2:160573/1‑143 (MQ=255)                                 cATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATCAAGGAAGGTGCCAATCAGCGGGGAAAGTCTTATCGGc                                                                                                        >  2:269600/1‑143 (MQ=255)                                   tttACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCAAATAAGCGGGGAAATTCTTCTCGGCTg                                                                                                      >  2:485644/1‑143 (MQ=255)                                        ccccacaGAAACGGAAAACCGTATCAGCATGAGTGATCCTGCGCGCCAATCAACAACCGTATCAGAATAGATACTGTCTTTAGGAATGTTTGTTTTATTAAGGAAGGTGCGAATTAGCGGGGAAATTCTTCTCGGCTGACTCa                                                                                                 <  2:509484/140‑1 (MQ=25)                                          gCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCACAATAGATACTTTCTTTAGGACTTTTTGTTTTATTACGGAAGGTGCGAATAAGCGGGGAAATTTTTCTCGGCTGACTCaat                                                                                               >  1:762319/1‑141 (MQ=255)                                              aaaaTCTGAAAAACGTACCAGCATAAATGTTCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatt                                                                                           <  1:612877/143‑1 (MQ=255)                                              aaaaTCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGtcatt                                                                                           <  1:163577/143‑1 (MQ=255)                                               aaaTCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCTAATAATCGGGGAAATTCTTCTCGGCTGACTCAGtcattt                                                                                          <  1:383969/143‑1 (MQ=255)                                                    tGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTcatttcattt                                                                                     <  1:267895/143‑1 (MQ=255)                                                        aaaCGTGCCAGCGTAAATGCTCCTGCGCACCAATCAACAACCGTATCAGAATAGATACGTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAGGAGGGCTGGGATATCGGTGCTGACTCAGTCATTTCATttcttc                                                                                 <  2:743563/143‑1 (MQ=255)                                                          aCGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGATTTTTTGTTGTATTAAGGCAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCAt                                                                               <  2:789777/143‑1 (MQ=255)                                                              aCCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGaaa                                                                                                                   >  1:847514/1‑103 (MQ=255)                                                              aCCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGaaa                                                                                                                   <  2:847514/103‑1 (MQ=255)                                                              aCCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTATGTTTTATTAAGGAAGGTGCGAATAAGCGGTGATATTCTTCTCTGCTGACTAAGTCATTTCATTTCTTCATGttt                                                                           >  2:906261/1‑143 (MQ=37)                                                                cAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGa                                                                         <  1:296146/143‑1 (MQ=255)                                                                  gCATAACTGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGc                                                                       <  1:198511/143‑1 (MQ=255)                                                                  gCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGc                                                                       <  2:747811/143‑1 (MQ=255)                                                                  gCATAAATCATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGc                                                                       <  1:419532/143‑1 (MQ=255)                                                                   cATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGcc                                                                      >  2:456607/1‑143 (MQ=255)                                                                   cATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGcc                                                                      >  1:590380/1‑143 (MQ=255)                                                                    aTAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATATCTACATGTTTGAGCCg                                                                     >  1:881180/1‑143 (MQ=255)                                                                     tAATTGATCCTGCTCATCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGa                                                                    <  2:738228/143‑1 (MQ=255)                                                                     tAAATGATCCTGCGCACCCATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGa                                                                    <  1:262882/143‑1 (MQ=255)                                                                         tGATCCTGCGCACCAATCAACTACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGTCTCAGTCATTTCATTTCTTCATGTTTGAGCCGAtttt                                                                <  2:254922/143‑1 (MQ=255)                                                                          gATCCTGCGAATCGTTCAACATCCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAttttt                                                               <  1:802494/143‑1 (MQ=21)                                                                            tCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTtc                                                             >  1:12029/1‑143 (MQ=255)                                                                                     ccAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCAAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTaaa                                                    <  1:485644/143‑1 (MQ=255)                                                                                      cAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAt                                                   >  1:449270/1‑143 (MQ=255)                                                                                       aaTCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATg                                                  >  1:596321/1‑143 (MQ=255)                                                                                          ctacaacCGTATCAGAATAGATCCCTTCTTTACGAATTTGTGTTTTATTAAGTAAGGTGCTAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCt                                               <  2:195479/141‑1 (MQ=18)                                                                                           gacaacCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCtt                                              <  1:27358/142‑1 (MQ=255)                                                                                           aacaacCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTGTTATTAAAGAAGGTGCGAATAAGCGGGGGAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCtt                                              >  1:592736/1‑143 (MQ=255)                                                                                               acCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAAt                                          <  1:244208/143‑1 (MQ=255)                                                                                                 cGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGACTAAGCGGGGAAATTTTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCTGATTTTTTCTCCCGTAAATGCCTTTAATCa                                        >  2:158844/1‑143 (MQ=255)                                                                                                   tATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTGTGTCGTTTGATTTCTTCGTGTTTGAGCCGATTTTTCCTCCCGTAAATGCGTTGGATCAGc                                      >  1:168414/1‑143 (MQ=18)                                                                                                   tATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTATATGTCCGGAATCacc                                      >  1:560036/1‑141 (MQ=255)                                                                                                        gAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTAATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTAtt                                 >  1:10027/1‑143 (MQ=255)                                                                                                         gaTAGATACTTTCTTTAGGAATTTTTGTTTTATTCAGGAAGGTGCGAATAAGCGGGGACATTGTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTGTTCTCCCGTAAATGCCTTGAATCAGCCTAttt                                <  2:364826/142‑1 (MQ=255)                                                                                                            aGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGa                             <  1:750992/143‑1 (MQ=255)                                                                                                              aTACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGAcc                           >  2:264910/1‑143 (MQ=255)                                                                                                                aCTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGACATTCTTCTCGACTGACTCAGTCATTTCATTTCTACATGTTTGAGCCGATTTTATCTCCCGTCACTGCTTTCACTCGACCTCTTTAGCCCGt                         >  2:302232/1‑143 (MQ=17)                                                                                                                aCTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGAAAATACTTCTCGGCTGACTCGAACATTTCATTTCTTAATGTTGGAGCCGATTGCTTCTCCCGTACATGCCTTGAATCCGCCTGTTTAGagggt                         >  1:338544/1‑139 (MQ=17)                                                                                                                  tttctttAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGttt                       >  2:411631/1‑143 (MQ=255)                                                                                                                  tttctttAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCCTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGttt                       <  1:37456/143‑1 (MQ=255)                                                                                                                      tttAGGAATTTTTGTTTTAGTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttcttc                   <  1:319231/143‑1 (MQ=255)                                                                                                                             aTTTTTGTTTTATTAAGGAAGGTCCGAATAAGCGGGGAAATTCTTCTCCGCTGACTCAGTCATTTCATTTCTTCATGTTCGCGCCGATTTTTTCTACCGTAAATGCCTTGAATCCGCCTCTTTATACCGTTTCTCCGCCAttt            >  2:854885/1‑143 (MQ=14)                                                                                                                               ttttGTTTGATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTaa          <  1:200255/143‑1 (MQ=25)                                                                                                                                   gTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCg      <  1:481775/143‑1 (MQ=35)                                                                                                                                    ttttATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGt     >  1:508323/1‑143 (MQ=34)                                                                                                                                     tttATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTTTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGtt    <  1:456607/143‑1 (MQ=18)                                                                                                                                       tattaAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAt  >  2:609949/1‑143 (MQ=32)                                                                                                                                             |                                                                                                                                         TTCACAGTACATAAAGTAACCTTGATCGAAGCCATTTACACGCACAAAATCTGAAAAACGTACCAGCATAAATGATCCTGCGCACCAATCAACAACCGTATCAGAATAGATACTTTCTTTAGGAATTTTTGTTTTATTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAT  >  NC_000913/2101609‑2101885

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.