New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2407180 =	0 (0.000)	30 (0.530)	30/486	0.7	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

TGGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAAC  >  NC_000913/2406945‑2407427                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                        ggccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGtt                                                                                                                                                                                                                                           >  1:116978‑M1/236‑250 (MQ=255) ggccatatcaatgattttctggtgcgtaccgggttgagaagcagtgtaagcgaactgcagttgccatgttttacggcagtgagagccgagatagcgctgctgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGttt                                                                                                                                                                                                                                          <  1:53248‑M1/16‑1 (MQ=255)   ccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcaggtgccatgttgtacggcagtgagaggagagatagcgctgatgtccttcggtgctgttgccgtgacgcaccaccccgtcagtagcggaacaggagggacatcttatagaaacagaagccacgggagcacctcagaaacaccatcatacactaaatcagtaagttggcggcgtcgccCGCTTAACAAGAGTTTca                                                                                                                                                                                                                                        >  2:202300‑M1/234‑251 (MQ=255)          aatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgtgttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTg                                                                                                                                                                                                                                 >  2:416426‑M1/227‑251 (MQ=255)           atgattttctggtgcgtaccgggttgagaagcggtgtcagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgcagttacgcaccaccccgtcaggagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggaagcatcaccCCCTTACCAATAGTTTCACAcctttc                                                                                                                                                                                                                                <  2:186105‑M1/26‑3 (MQ=255)                     ggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcgtttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcttcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCg                                                                                                                                                                                                                      >  1:82964‑M1/216‑251 (MQ=255)                          gtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagcttaacaggagggacagctgatataaacagaagccactggagcacctcaaaaacaccatcatgctctaaaacagtaagtgggcatcaccacgCGCGTAACAATAGTTTCACACCTTGCCCCCATTGCGACAcc                                                                                                                                                                                                                 >  1:248187‑M1/211‑251 (MQ=255)                             ccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgtgacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACTCCTTGCCCCCATTGCGACACCTCg                                                                                                                                                                                                              >  1:70844‑M1/208‑251 (MQ=255)                                   ggagaagcggtggaagtgaacggcagtggccatgtgttacggcagtgagagcagagagagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTGAAACACCTTGCCCGCATTGCGACACCTCTGAAatc                                                                                                                                                                                                        >  2:78922‑M1/202‑251 (MQ=255)                                         gcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgataggaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACg                                                                                                                                                                                                  <  1:338340‑M1/56‑1 (MQ=255)                                         gcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACg                                                                                                                                                                                                  >  2:61190‑M1/196‑251 (MQ=255)                                                                       ttacggcagtgagagcagagatagcgctgatggccggcggtgcttttgccgttacgcacaaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCAATGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAatat                                                                                                                                                                     >  2:395421‑M1/166‑250 (MQ=255)                                                                           ggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATatcatc                                                                                                                                                                 <  1:126577‑M1/89‑1 (MQ=255)                                                                            gcaggtagagcacagatagcgctgagggccggcggtgctgttgccgttacgccccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccgctggagcccctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATatcatcat                                                                                                                                                               >  2:119693‑M1/161‑251 (MQ=255)                                                                              agtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacaataaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATcg                                                                                                                                                             <  1:280618‑M1/93‑1 (MQ=255)                                                                                         agatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgataggaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGGAATGAGGAAATATCATCATCGCGTTTCATTAg                                                                                                                                                  >  2:338340‑M1/148‑251 (MQ=255)                                                                                               cgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCAGCGCGTTTCATTAGTGAAtt                                                                                                                                            >  1:450542‑M1/142‑251 (MQ=255)                                                                                                                      gccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagtttgcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCGCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCTCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTcacac                                                                                                                      >  2:221285‑M1/119‑250 (MQ=255)                                                                                                                            acgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTGTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATc                                                                                                               >  1:242926‑M1/113‑251 (MQ=255)                                                                                                                              gcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcaggaagttggcagcatcaccCGCTTAACAATAGTTGCACACCTTGCCCCCAGTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTTAATTCTTAAATGAGGCATTTTCACACAATTATCtt                                                                                                             >  2:357463‑M1/111‑251 (MQ=255)                                                                                                                                           agtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATaaaaaa                                                                                                 <  1:212486‑M1/153‑1 (MQ=255)                                                                                                                                                   aacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACtt                                                                                        >  1:322515‑M1/90‑251 (MQ=255)                                                                                                                                                     caggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCCTACATATAAAAAAACCAGACTTAc                                                                                      >  1:186105‑M1/88‑251 (MQ=255)                                                                                                                                                        gagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAAt                                                                                   <  1:131701‑M1/167‑1 (MQ=255)                                                                                                                                                         agggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcgccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGGTTCAGTAGTGAATTCTTAAATGATGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAAtt                                                                                  >  1:341772‑M1/84‑251 (MQ=255)                                                                                                                                                              cagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATgaagaa                                                                             >  2:385108‑M1/79‑251 (MQ=255)                                                                                                                                                                            agaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCAc                                                               <  1:51512‑M1/187‑1 (MQ=255)                                                                                                                                                                                                                    aatcagttagcttgcagcatcacccGCCTAACAATATGTTCGCACCTTGCCCACATTGCTCCAACTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAAGGTGGCATTGTCACACAATGATCTTACATATAAAAAAACCAGACTTACAATTTATAATCAGAACAATCCACTATATAACATTGCATGTCAAGCATATACCCCTCtttattg                       <  2:281339/228‑2 (MQ=255)                                                                                                                                                                                                                               tggcagcatccccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCAGGTAAAGCATATACACCTCATTATTTTGTCattatt             >  2:85704‑M1/14‑250 (MQ=255)                                                                                                                                                                                                                                      atcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGttatt     >  1:526903‑M1/7‑251 (MQ=255)                                                                                                                                                                                                                                         accCGCTTAACAATAGTTTCACACCTTGCCCCCATCGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAAc  <  2:340373‑M1/248‑1 (MQ=255)                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                        TGGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAAC  >  NC_000913/2406945‑2407427

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.