New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2407180 =	0 (0.000)	27 (0.880)	25/488	0.3	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                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                        ggccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGttt                                                                                                                                                                                                                                          >  1:200540‑M1/236‑251 (MQ=255)                                      gaatcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagtttgcagcatcaccCGCTTAACAATAGGTTCACACCTTGCCCCCATTGCGACACCTCGGAAatcatc                                                                                                                                                                                                     >  1:157345‑M1/199‑251 (MQ=255)                                                      actgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACtctc                                                                                                                                                                                     >  2:33290‑M1/183‑251 (MQ=255)                                                                  atgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGGTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGa                                                                                                                                                                          <  2:7329‑M1/80‑1 (MQ=255)                                                                    gttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGaaa                                                                                                                                                                        >  1:94194‑M1/169‑250 (MQ=255)                                                                    gttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTGAAACTCTCCGTAATGAGGAAat                                                                                                                                                                       >  1:58400‑M1/169‑251 (MQ=255)                                                                        tacggcagtgagagcagagatagcgctgatgtccggcggtgcgttggccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccTGCTTAACAATAGTTTCATACCTTGCCCCCATTGCGACACCGGGGAAATCATcacgcagttgaactctccttatggagcaaatatc                                                                                                                                                                    >  2:177506‑M1/165‑234 (MQ=255)                                                                         ccggcagtgagagcagagatagcgctgatggccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCAGCACGCAGTTAAACTCTCCGTAATGAGGAAATatcat                                                                                                                                                                  >  2:108517‑M1/164‑251 (MQ=255)                                                                                     gcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACGCCTTGCCCCCATTGCGACACCTCGGAAATCATCTCGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCa                                                                                                                                                      >  1:143190‑M1/152‑251 (MQ=255)                                                                                      cagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCAt                                                                                                                                                     >  1:20159‑M1/151‑251 (MQ=255)                                                                                          gatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGt                                                                                                                                                 >  1:205566‑M1/147‑251 (MQ=255)                                                                                             agcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaataagtaagttggcagcatcaccCGCTTCACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGa                                                                                                                                               <  2:296655‑M1/107‑1 (MQ=255)                                                                                                    atgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACTCCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAAGGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTaa                                                                                                                                       >  1:189453‑M1/137‑251 (MQ=255)                                                                                                              gtgcttgtgcctgtacgcaccaccccttcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaactccatcatacactgaagcagtaagttggcggcataaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAAACATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGGTTCATTAGGGAATTCTTAAATGAGGCAtt                                                                                                                             >  2:299141‑M1/127‑251 (MQ=255)                                                                                                                         gttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAAtt                                                                                                                  <  1:298931‑M1/136‑1 (MQ=255)                                                                                                                         gttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAAtt                                                                                                                  >  2:207803‑M1/116‑251 (MQ=255)                                                                                                                            acgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAAGGAGGCATTTTCACACAATTAt                                                                                                                >  1:88856‑M1/113‑250 (MQ=255)                                                                                                                                                  gaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACt                                                                                         <  1:3977‑M1/161‑1 (MQ=255)                                                                                                                                                           ggacagctgatagaaacagaagccactggagcacctccaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCCTTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACttacactta                                                                                 <  1:211960‑M1/169‑5 (MQ=255)                                                                                                                                                                           cagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCa                                                                >  1:139496‑M1/66‑251 (MQ=255)                                                                                                                                                                              aagccactggagcaactcaaaaacaccatcatacactaaatgagtaagtttgcagcatcaccCGCTTAAAAATAGTTTCACACCGTGCCACCAGTGCGACACCTCGGAAATCAGCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGGTTCAGTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCGGACAGATAAAAAAACCAGACCTACAATTAAGAaacagaacacttcccta                                                             >  2:15187‑M1/63‑243 (MQ=255)                                                                                                                                                                                             ctcaaaaacacaatcatacactaactcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTCATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGt                                              <  2:116719‑M1/204‑1 (MQ=255)                                                                                                                                                                                               caaaaacaccatcatacactaaatcagtaagttggcagcatcaccCTCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTGCAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTaa                                            >  1:7233‑M1/46‑251 (MQ=255)                                                                                                                                                                                                   aacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCa                                        >  1:296655‑M1/42‑251 (MQ=255)                                                                                                                                                                                                                               tggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGGTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCGTACAGATAAAAAAACCAGACTTACAAGGAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCattatt             >  1:283292‑M1/14‑250 (MQ=255)                                                                                                                                                                                                                                ggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAAGCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTaa           >  1:133140‑M1/13‑251 (MQ=255)                                                                                                                                                                                                                                         accCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTGTGTCATTATTAAGTTATTAAc  >  2:211960‑M1/4‑251 (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.