New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2407180 =	0 (0.000)	37 (0.720)	32/490	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

TGCAGCATCGCTGGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTA  >  NC_000913/2406934‑2407425                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                      acgccattcatggccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggcgcttttgccgttacgcaccaccccgtcagtagctgaacaggagtgacagctgatagaaacagaagccactggagcacctcaacaacaccatcatacactaaatcagtaagctggcagcatcaccCGCtt                                                                                                                                                                                                                                                   <  2:41379‑M1/5‑1 (MQ=255)   gcaattcatggccatatcaatgattttctggtgcgtaccgggttgagaagcggtggaagtgaactgcagtttccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgtcgttacgcaccaccccgtcagtagctgaacaggaggtacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacacttaatcagtaagtttgcagcatctccCGCTTaa                                                                                                                                                                                                                                                 >  2:387037‑M1/245‑251 (MQ=255)    ccattcatggccatatccatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggaagtgagagcagagatagcgctgatgtacggcggggcttttgccgttacgcaccacaccgtccgtagctgaacaggcgggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactcaataaggaagttggcagcatcaccCGATTAAc                                                                                                                                                                                                                                                <  2:348957‑M1/8‑1 (MQ=255)            ggccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGttt                                                                                                                                                                                                                                        >  1:393345‑M1/236‑251 (MQ=255)            ggccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGtt                                                                                                                                                                                                                                         >  1:94604‑M1/236‑250 (MQ=255)                       tgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgctacgcaccaccccggcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaacatcatacactaaatcaagaagttggcagcatcaccCGCTTAACAATAGGTtcacaccatacc                                                                                                                                                                                                                             <  2:280546‑M1/27‑6 (MQ=255)                              ctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTg                                                                                                                                                                                                                      <  2:144475‑M1/34‑1 (MQ=255)                                  ggcgtaccgggttgagaagcgtggtaagtgaactgcagttgccatgttttacggctgtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacatgagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatctccCGCTTAACAATAGTTTCACACCTTGCCCCCAttgctac                                                                                                                                                                                                                  >  2:234518‑M1/214‑248 (MQ=255)                                       accgggttgagaagcggtgtaagggaactgcagttgccatgttgtacggcagtgatagcatagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagtgacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatccccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCt                                                                                                                                                                                                              >  2:251595‑M1/209‑250 (MQ=255)                                          gggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCgg                                                                                                                                                                                                           <  1:228625‑M1/45‑1 (MQ=255)                                          gggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCgg                                                                                                                                                                                                           <  1:7212‑M1/45‑1 (MQ=255)                                               gagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAatc                                                                                                                                                                                                      <  1:247810‑M1/50‑1 (MQ=255)                                                 gaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAatcatc                                                                                                                                                                                                   >  2:262845‑M1/199‑251 (MQ=255)                                                    gcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACg                                                                                                                                                                                                <  1:182362‑M1/56‑1 (MQ=255)                                                         gtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGt                                                                                                                                                                                            >  1:43430‑M1/191‑250 (MQ=255)                                                                                   tacggcagggagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGaaatagc                                                                                                                                                                  >  2:7212‑M1/165‑248 (MQ=255)                                                                                    acggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCTACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGTAAATatcat                                                                                                                                                                >  1:249255‑M1/164‑251 (MQ=255)                                                                                          gtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaccagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGCCACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATcgc                                                                                                                                                          <  2:394153‑M1/94‑1 (MQ=255)                                                                                              gagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGttt                                                                                                                                                      >  1:299233‑M1/154‑251 (MQ=255)                                                                                                     aatagcgctgaggtccgccggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccacttgagcacctcaaaaacaccatcattcactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACTCCTTGCCCCCATTGCTACACCTCGGAAATCATCACGCATTTAAACGTTCGGTAAGGAGGAAATCTCATCATCGCGTTTCATTagg                                                                                                                                               >  2:345779‑M1/147‑250 (MQ=255)                                                                                                              gatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTa                                                                                                                                      >  1:405834‑M1/138‑251 (MQ=255)                                                                                                              gatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTa                                                                                                                                      >  1:400011‑M1/138‑251 (MQ=255)                                                                                                                 gtccggcggtgcttttgccgttacgcgccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAAt                                                                                                                                   >  1:18058‑M1/135‑251 (MQ=255)                                                                                                                              tttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACCATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTcac                                                                                                                      <  1:88124‑M1/130‑1 (MQ=255)                                                                                                                                                         agctgaacagtagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAAcc                                                                                            >  2:127654‑M1/95‑250 (MQ=255)                                                                                                                                                              aacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACtt                                                                                      >  1:411161‑M1/90‑251 (MQ=255)                                                                                                                                                                           gctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAAGGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATc                                                                         >  1:113322‑M1/77‑251 (MQ=255)                                                                                                                                                                                              actggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACACTTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACtatata                                                       <  2:265171‑M1/193‑1 (MQ=255)                                                                                                                                                                                                     cacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACa                                                                                   >  2:161783‑M1/51‑215 (MQ=255)                                                                                                                                                                                                     cacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACa                                                                                   <  1:161783‑M1/165‑1 (MQ=255)                                                                                                                                                                                                          caaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTaa                                          >  1:144475‑M1/46‑251 (MQ=255)                                                                                                                                                                                                           aaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTaa                                          <  1:316094‑M1/206‑1 (MQ=255)                                                                                                                                                                                                                caccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCat                                     <  1:109277‑M1/211‑1 (MQ=255)                                                                                                                                                                                                                              aaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCattat                       >  2:440798‑M1/26‑250 (MQ=255)                                                                                                                                                                                                                                   agtgagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGTGACACCTCGGAAATCCTCACGCAGTTAAACTCTCCGTAATTAGGAAATATCATCATCACGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTATAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTTACTATATAACATTGCATTTAAAGCTTATACATCTCATTATTTTg                   >  2:341210‑M1/21‑249 (MQ=255)                                                                                                                                                                                                                                       agttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCatt              <  2:47754‑M1/234‑1 (MQ=255)                                                                                                                                                                                                                                                   caccCGCGTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGttatta  >  2:69925‑M1/5‑250 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                      TGCAGCATCGCTGGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTA  >  NC_000913/2406934‑2407425

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ 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.