New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2407180 =	0 (0.000)	38 (1.130)	35/484	0.1	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

GGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACC  >  NC_000913/2406946‑2407397                                                                                                                                                                                                                                           |                                                                                                                                                                                                                          gccatctcaaggattttctggtgcgtaccgggtggagaagcggtgtaagttaactgcagatgccatggtttacggcaggtagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcacctacccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggatcacctcaaaaacaccatcatacactaaagcagtaagttggcagcatcaccCGCTTAACAATAGTTTc                                                                                                                                                                                                           >  2:47261‑M1/235‑251 (MQ=255)                           accgggttgagaagcggtgtaagtgaactgcagttgccatgatttacggcagtgagagcagagatagcgctgatgtccggcggagcttttgccgttacgcacccccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactcgagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTc                                                                                                                                                                                 <  1:316451‑M1/43‑1 (MQ=255)                                      aagcggtggaagtgaagtgcagttgtcatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccacaccgtcagtagctgaacaggagggacagctgatagacacagaagacactggagcacctcaaaaacaccatcataaactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACAACTTGCCCCCATTGCGACAACGCGGAAatcatc                                                                                                                                                                       <  2:242987‑M1/53‑1 (MQ=255)                                                 gtgaactacagttgccttgttttacggatgtgcgagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccggcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacaataaatcagtaagttggcagcatcaccCGCTTAACAATAGCTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAAc                                                                                                                                                           <  2:34073‑M1/65‑1 (MQ=255)                                                   gaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAAct                                                                                                                                                          >  1:102432‑M1/185‑250 (MQ=255)                                                    aactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAActct                                                                                                                                                        <  1:250199‑M1/68‑1 (MQ=255)                                                           ggtgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAAt                                                                                                                                                 >  2:11209‑M1/177‑251 (MQ=255)                                                                  tgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGaa                                                                                                                                           <  1:21250‑M1/81‑1 (MQ=255)                                                                   gttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAat                                                                                                                                         <  1:161660‑M1/83‑1 (MQ=255)                                                                     tttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAata                                                                                                                                        >  1:328377‑M1/167‑250 (MQ=255)                                                                        acggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATAATCACGCAGTTAAACTCTCCGTAATGAGGAAATatcat                                                                                                                                    <  1:50296‑M1/88‑1 (MQ=255)                                                                            cagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATatcatcatc                                                                                                                                >  1:211128‑M1/160‑251 (MQ=255)                                                                                 agagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGCAATATCATCATCGCGtt                                                                                                                           <  2:82657‑M1/97‑1 (MQ=255)                                                                                 agagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGtt                                                                                                                           <  2:275904‑M1/97‑1 (MQ=255)                                                                                  gagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATAGCATCATCGCGttt                                                                                                                          >  1:286527‑M1/154‑251 (MQ=255)                                                                                      agagatagcgctgacgtccgtcggggcttttgccgttacgcccccacccgtcagtagctgcacaggagggacagctgatagaaacagaaaccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACCACTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGCGGAAATATCATCATCGCGTTTCAtt                                                                                                                      <  2:333344‑M1/102‑1 (MQ=255)                                                                                         gatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGt                                                                                                                   >  2:161660‑M1/147‑251 (MQ=255)                                                                                            agcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGaa                                                                                                                >  1:269240‑M1/144‑251 (MQ=255)                                                                                               gctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtcgctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTc                                                                                                             <  2:164019‑M1/111‑1 (MQ=255)                                                                                                 tgatgtcaagcggagcttttgccgttacgcaccaccccgtcagtcgctgaacaggcgggacagctgatagaaacagaagcccctgcagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaacCGCTTAACAATAGTTTCACACCTTGACCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATTAGGAACTCTCCTCATCGCGTTTCATTAGTGAATTCtt                                                                                                           <  2:206378‑M1/113‑1 (MQ=255)                                                                                                  gatggccggcggttcgttggccgttacgctccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTTCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAAGATCATCATCTCGTTTCATTAGTGAATTCt                                                                                                            >  2:229415‑M1/138‑249 (MQ=255)                                                                                                                cctttgccgttacgcaccaccccgtcactagctgaacaggagggacagctgatagaaacagaagccactggggcacctcaaaaacaccatcattcactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATGTCGACACCTCGGAAATCATCACGCAGTTAAACTCTTCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATGCTTACATGAGGGATTTTc                                                                                            >  2:223797‑M1/124‑251 (MQ=255)                                                                                                                           acgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTAt                                                                                  >  2:119814‑M1/113‑250 (MQ=255)                                                                                                                                          agtagctgaacaggggggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCAt                                                                                                                                                                                            <  1:75096‑M1/32‑1 (MQ=255)                                                                                                                                          agtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCAt                                                                                                                                                                                            >  2:75096‑M1/98‑129 (MQ=255)                                                                                                                                                 gaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCGTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCGCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATGAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACt                                                           >  2:50296‑M1/91‑251 (MQ=255)                                                                                                                                                    caggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTAc                                                        <  2:240963‑M1/164‑1 (MQ=255)                                                                                                                                                        agggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAAtt                                                    >  1:194612‑M1/84‑251 (MQ=255)                                                                                                                                                          ggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTaa                                                  >  2:250199‑M1/82‑251 (MQ=255)                                                                                                                                                          ggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTaa                                                  >  1:164019‑M1/82‑251 (MQ=255)                                                                                                                                                               gctgagagaaacagaagccactggagcacctcaaaaacaccagcatacactaaatcagtaagttgcccgcatcaccCGCTTAACAATAGCTTCACTCCTTGCCCCCATTGCGACACCTCGTAAATCATCACTCAGTTAAACTCTCCGTAATGAGGAAATATCAACATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATc                                             >  2:318221‑M1/77‑251 (MQ=255)                                                                                                                                                                                 cactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATGCACtatata                           >  1:110109‑M1/59‑251 (MQ=255)                                                                                                                                                                                    tggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTc                                                                                            <  2:117020‑M1/128‑1 (MQ=255)                                                                                                                                                                                    tggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTc                                                                                            >  1:117020‑M1/56‑183 (MQ=255)                                                                                                                                                                                          acctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCAt                  >  1:240963‑M1/50‑251 (MQ=255)                                                                                                                                                                                                          catacactaaatcaggaagttggcagcagcacgCGCTTAACAATAGTTTCACACCTTGCCCCCCTTGCGACACCTCGGAAATAATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCCTTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGCTAAAAAAACCAGACTTACAATTAAGAAGCAGAACAATTCACTATATACCATTGAATGTAAAGCATATACAcc  <  2:122926‑M1/218‑1 (MQ=255)                                                                                                                                                                                                                                 cagcatcaccCGCTTAACAATAGTTTCACACCTTGCCACCATTGCGACACCTCGGAAATCATCACGCCGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTcacac                                                                                        <  1:306533‑M1/132‑1 (MQ=255)                                                                                                                                                                                                                                 cagcatcaccCGCTTAACAATAGTGTCACACCTTGCCCCCATGGCGACACCTCGGAAATCATCACGCAGTAAAACTCTCCGTAATGAAGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAAAGAGGCATTTTcacac                                                                                        >  2:306533‑M1/11‑142 (MQ=255)                                                                                                                                                                                                                                           |                                                                                                                                                                                                                          GGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACC  >  NC_000913/2406946‑2407397

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ 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.