New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2407180 =	0 (0.000)	38 (0.590)	36/488	0.4	100%	intergenic (‑539/‑381)	lrhA/alaA	DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA
	?	NC_000913	3583428 =	NA (NA)					noncoding (1/768 nt)	IS1	repeat region

GCATCGCTGGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAG  >  NC_000913/2406938‑2407419                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                cattcatggccatatcaatgattttctggtgcgtaccggtttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggccagctgatagcaacagaaaccactggagcacctcaaaaacaacatcataccccaaatccgtaagttggaaccatcaccCGCTTAAc                                                                                                                                                                                                                                          <  1:214281‑M1/8‑1 (MQ=255)    tcatggccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAAt                                                                                                                                                                                                                                       >  1:57134‑M1/240‑250 (MQ=255)         gccatatcaatgattttctggtgcgtaccggggtgagaagtggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaacccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaaggtggcagcatcaccCGCTTAACAATAGTTTc                                                                                                                                                                                                                                 >  2:335645‑M1/235‑251 (MQ=255)              atcaatgattttcttgtgcttatcgggttgagaagcggtgtaagggaactgtagttgccatgttttacggcagtgagagcagagatagcgctgttgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACAcc                                                                                                                                                                                                                            >  2:410551‑M1/230‑251 (MQ=255)                                 gtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTCCGACAcc                                                                                                                                                                                                         <  1:324332‑M1/41‑1 (MQ=255)                                   cccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGActcctc                                                                                                                                                                                                       >  1:272483‑M1/209‑251 (MQ=255)                                          tgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAat                                                                                                                                                                                                 >  1:243775‑M1/202‑250 (MQ=255)                                                          tgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAAct                                                                                                                                                                                <  1:458232‑M1/66‑1 (MQ=255)                                                           gatctgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgatcaggagggacagctgatagaaacagaagccactggatcacctcaaaaacaccatcatacactaaatcagtaagttgtctgcatcaccCTCTTAACAATATTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAAct                                                                                                                                                                                >  1:181536‑M1/185‑250 (MQ=255)                                                            aactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcgccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacaccaaatcagtacgttggcagcatcaccCGCTTAACAATAGTTTCACCCCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAActct                                                                                                                                                                              >  1:313182‑M1/184‑251 (MQ=255)                                                                 cagttgccatggtttacggcagtgagagcagagatagcgctgatgtcaggcggtgcttgtgccgttacgcaccaccccgtcagtagcggaacaggagtgtcagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACTCCTGGCCCCCATTGCGACACCTCGGAAATCATCTCGCAGTTAAACTCTCCGTa                                                                                                                                                                         >  2:384208‑M1/179‑251 (MQ=255)                                                                  agttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcacccccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcaccacaaaaacaccatcatacactaaatcagtaagtttgcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTaa                                                                                                                                                                        >  2:486281‑M1/178‑251 (MQ=255)                                                                     tgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccggtacgcaccaccccgtcagtagctgaacaggagggaacgctggtagaaacagaaaccaattgagcacctccaaaacaacatcatacactaaatccataagatggcagcatcaccAGCTTAACAATAGTTTCACACCTTGACCCCATTGCGACACCTCGGAAATCAGCACGAAGTTAAAATCTCCGTaa                                                                                                                                                                        <  2:365124‑M1/74‑1 (MQ=255)                                                                      gccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGa                                                                                                                                                                     >  1:263493‑M1/174‑250 (MQ=255)                                                                           gttttacggcagtgagagcagagatatcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAat                                                                                                                                                               >  2:361743‑M1/169‑251 (MQ=255)                                                                                acggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATatcat                                                                                                                                                          >  1:126649‑M1/164‑251 (MQ=255)                                                                                      gtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATcgc                                                                                                                                                    <  1:445330‑M1/94‑1 (MQ=255)                                                                                        gagagcagagatagcgctaatgtccggcggtgcttttgccgttccgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccagcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTACGTAATGAGGAAATATCATCATCGCGt                                                                                                                                                  >  2:375717‑M1/156‑251 (MQ=255)                                                                                           agcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTc                                                                                                                                               <  1:276585‑M1/99‑1 (MQ=255)                                                                                                  atagcgctgatgtgcggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCAACACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTg                                                                                                                                        >  1:325867‑M1/146‑251 (MQ=255)                                                                                                    agcgctgatgtccggcggtgcttttgccgttaagcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggcgcaccacaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAAATCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGa                                                                                                                                       <  1:172675‑M1/107‑1 (MQ=255)                                                                                                      cgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGCGGAAATATCATCATCGCGTTTCa                                                                                                                                              <  2:494355‑M1/100‑1 (MQ=255)                                                                                                      cgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCa                                                                                                                                              >  1:494355‑M1/142‑241 (MQ=255)                                                                                                                   gggtgctgttgccggtaagtaccaccccttcagtagctgaacaggagggacagcgtatagaaacagaagacactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcggcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGgct                                                                                                                       >  2:535303‑M1/129‑250 (MQ=255)                                                                                                                           ttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACTCCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTcac                                                                                                                >  1:506018‑M1/121‑250 (MQ=255)                                                                                                                                    cgcaccaccccttcagtagctgaacaggagggacagctgataaaaaaagaagccactgtagccccacaaaaactccatcatacactaaatcagtaagttgtcagcatcaccCGCTTAACAATAGTTTCACTCCTTGCCCCCATTGCGACTCCTCGGAAATCATCACGCAGTTAAACTCTACGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCTTTTTCACACAATTATCt                                                                                                      >  2:539998‑M1/112‑251 (MQ=255)                                                                                                                                                                agggacagatgatagaaacagcagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCACATTGCGACACCACGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAAtt                                                                          >  2:346219‑M1/84‑251 (MQ=255)                                                                                                                                                                    acagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTa                                                                         <  1:308943‑M1/169‑1 (MQ=255)                                                                                                                                                                             agaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGCCACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCTTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACACTTATCTTACAGATAAAAAAACCAGCCTTACAATTAAGAATCAGAAc                                                              <  2:513355‑M1/180‑1 (MQ=255)                                                                                                                                                                               aaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAAt                                                           >  1:323769‑M1/69‑251 (MQ=255)                                                                                                                                                                                  cacaagcctcgggagcacctcaaaaacaccatcagacactaaatcagtaagttggcagcatccccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCGCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCa                                                        >  2:458232‑M1/66‑251 (MQ=255)                                                                                                                                                                                       gccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACtat                                                    <  1:144418‑M1/190‑1 (MQ=255)                                                                                                                                                                                                       aaaaacacaatcataaactaaatcagtacggtggcagcatcaccCGCTTAACAATAGTTTCACCCCTTACCCCCATTGCGACCCCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGCAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAACACACAGACTTACACTTAAGAATCAGAACAATTCACTATATAACATTGCATGTaa                                    <  2:326976‑M1/206‑1 (MQ=255)                                                                                                                                                                                                                      cactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCat                    >  1:84413‑M1/30‑251 (MQ=255)                                                                                                                                                                                                                      caataaatcagtaagttggcagcatcaccAGCTTAACAATAGTTTCACACCTTGCCCACATTGCGACACCTAGGAAATCATCACGCAGTTAAACTCTCAGTAATGAGGAAATATCATCATCGCGTTTCATTAGAGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATAAACCTCat                    <  2:316232‑M1/222‑1 (MQ=255)                                                                                                                                                                                                                            atcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTAtttt              >  1:402061‑M1/24‑251 (MQ=255)                                                                                                                                                                                                                            atcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTAtttt              <  1:358194‑M1/228‑1 (MQ=255)                                                                                                                                                                                                                                        gcagcaacaccCGCTTAACAATAGTTTCACACCCTGCCCCCAGTGCGACACCTCGGAAATCATCACGCAATTAAACTCTCCGTAATGAGGAAATATCATCACCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTAGCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAGCAATTCTCTATATAACTTTGCATGTAAAGCATATACACCTCATTATTTTGGCATTATTAAg  >  1:513079‑M1/12‑251 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                GCATCGCTGGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAG  >  NC_000913/2406938‑2407419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ 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.