New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2407180 =	0 (0.000)	36 (0.790)	35/482	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

GCAGCATCGCTGGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTA  >  NC_000913/2406935‑2407422                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   cgccattcatggccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCtt                                                                                                                                                                                                                                                <  1:155004‑M1/5‑1 (MQ=255)  gccattcatggccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTaa                                                                                                                                                                                                                                              >  1:191708‑M1/245‑251 (MQ=255)   ccagtcatggccatatcaaggattttctggtgggttccgggttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcagcaccCGCTTAAc                                                                                                                                                                                                                                             >  2:406222‑M1/244‑251 (MQ=255)         atggccatatcaatgattttctggtgcgtaccgggttgagaagcggtgtaagtgaactgaagttgccatgttttacggcagtgagagcagagctagcgctgatgtccggcggtggttttgccggtacgcaccaccccgtcaggtgatgaacaggagggacagctgatagaaacagaagacactggagcacctcaaaaaccccatcatacactaaattagtaagatggcagcctcaccCGCTTAACAATagg                                                                                                                                                                                                                                       <  2:12945‑M1/14‑2 (MQ=255)                     atgattttctggtgcgtaccgggttgagaagcggtttaagtgaactgcagttgccatgtttgacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgccccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGc                                                                                                                                                                                                                           >  2:353990‑M1/226‑251 (MQ=255)                                           gttgagaagcggtgtaagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGaa                                                                                                                                                                                                      <  1:318785‑M1/47‑1 (MQ=255)                                                  agcggtgtaatgtaactgcaggtgccatggtgtacggcagtgagagcagagatagcgctgatgtccggctgtgcttttgccgttacgccccaccccgtcaggagctgaaaaggagggacagctgatagaaacagaagccactggggcacctcaaaaacaccatcatacactaaatcagtaagttggcatcaccgccCGCTTAACAATAGTTTCACGCCTTGCCCCCATTGCGACACCTCGGAAAACATCAc                                                                                                                                                                                              >  2:82781‑M1/197‑251 (MQ=255)                                                  agcggtgtaagtgaactgcagttgccatgttttacggccgtgagagccgagatagcgctgatgtccgccggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCAc                                                                                                                                                                                              <  1:303997‑M1/55‑1 (MQ=255)                                                          aagtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTaa                                                                                                                                                                                      >  2:155004‑M1/189‑251 (MQ=255)                                                            gtgaactgcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAAc                                                                                                                                                                                    >  1:258609‑M1/187‑251 (MQ=255)                                                                   gcagttgccatgttttacggcagtgagagcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTcc                                                                                                                                                                               >  2:15387‑M1/180‑249 (MQ=255)                                                                                             gggcagagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacgccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATATTGTCACACCTTGCCCC‑ATTGCGACACCTCGGAAATCAGCACGCAGTTAAGCTCTCCGTAATGAGGAAATATCGTCATCGCGTTTc                                                                                                                                                  >  2:278001‑M1/154‑251 (MQ=255)                                                                                                 agagatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCAtt                                                                                                                                               <  1:441482‑M1/102‑1 (MQ=255)                                                                                                   agatagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTTTCCGTAAGGAGGAAATATCAGCATCGCGTTTCATTAg                                                                                                                                             >  1:154436‑M1/148‑251 (MQ=255)                                                                                                     atagcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTg                                                                                                                                           <  1:68466‑M1/106‑1 (MQ=255)                                                                                                     atagcgctgatggccggcggtgcttttgccggtacgcaccaccccgtcagtagctgaacaggagggacagctgaaagaaacagaagccagtggagcacctcaaaatcaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCGTGCCCCCATTGCGGCACCTCGGAAAGCATCACGCAGTTAAACTGTCCGTAATGAGGAAATATCATCATCTCGTGTCATTAGTg                                                                                                                                           >  2:268811‑M1/146‑251 (MQ=255)                                                                                                        gcgctgatgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCTTAATGAGGAAACATCATCATCGCGTTTCATTGGTGAAt                                                                                                                                        >  1:359492‑M1/143‑251 (MQ=255)                                                                                                             gatgtccggcggtgcttttgccgtttcgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccagcatacactaaatcagtaagttggcatcatcaccCGCTTAACAATAGTTTCACGCCGGGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAGTTCTGCTTAATTAGGAAATATCATCATCGCGTTTCATTAGTGAATTCtt                                                                                                                                    >  1:224053‑M1/138‑250 (MQ=255)                                                                                                              atgtccggcggtgcttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTaa                                                                                                                                  >  2:68466‑M1/137‑251 (MQ=255)                                                                                                                            ttttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTc                                                                                                                     <  1:117243‑M1/128‑1 (MQ=255)                                                                                                                             tttgccgttacgcaccaccccgtcagtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGGGAAGTCTTAAATGAGGCATTTTc                                                                                                                     >  2:80611‑M1/122‑249 (MQ=255)                                                                                                                                  cgtcacgcaccaccccgtcagttgctgaacaagagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatctccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTACTTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATTAGGCATTGTCACACAAt                                                                                                              >  2:203778‑M1/117‑251 (MQ=255)                                                                                                                                   gttacgcaccaccccgtcagtagctgaacaggagggaccgctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTACATGCGGCATTTTCACACAAtt                                                                                                             <  1:410793‑M1/136‑1 (MQ=255)                                                                                                                                   gttacgcaccaccccgtcagtagctgaacaggagggacagcttatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcagcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAAtt                                                                                                             >  2:117243‑M1/116‑251 (MQ=255)                                                                                                                                                      gtagctgaccaggagggacagctgatcgaaccagaagccactggagcacctcaaaaacaccatcatacactaaatcagtacgttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAata                                                                                                                                                                 <  2:376135‑M1/84‑1 (MQ=255)                                                                                                                                                      gtagctgaacaggagggacagctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACTCAGTTAAACGCTCCTTAATTAGGAAata                                                                                                                                                                 >  1:376135‑M1/97‑180 (MQ=255)                                                                                                                                                                         agctgatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAATGAATTCTTAAATGAGGCATTTTCACACAATTAGCTTACAGATAAAAAAACCAGACTTACAATTAAGAAt                                                                       >  2:441482‑M1/78‑251 (MQ=255)                                                                                                                                                                             gatagaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATc                                                                      <  2:333106‑M1/175‑1 (MQ=255)                                                                                                                                                                                agaaacagaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAAc                                                                 >  2:403200‑M1/71‑250 (MQ=255)                                                                                                                                                                                      agaagccactggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCAc                                                          >  1:101447‑M1/65‑251 (MQ=255)                                                                                                                                                                                                ggagcacctcaaaaacaccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAAc                                                  >  1:167526‑M1/55‑249 (MQ=255)                                                                                                                                                                                                                cccatcatacactaaatcagtaagttggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCATAACAATTCACTATATAACATTGCATGTAAAGCatat                                >  1:35735‑M1/39‑251 (MQ=255)                                                                                                                                                                                                                   atcatacactaaatcagtaaggtggcagcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATaca                             >  2:103564‑M1/36‑251 (MQ=255)                                                                                                                                                                                                                              aatcagtaagttggcagcatcaccCGCTTAACAAGAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCAACGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCAGGTAAAGCATATACACCTCATTAttt                  >  2:230073‑M1/25‑251 (MQ=255)                                                                                                                                                                                                                                              gcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGtta  >  1:340831‑M1/9‑251 (MQ=255)                                                                                                                                                                                                                                              gcatcaccCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACGTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGtta  >  2:318785‑M1/9‑251 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   GCAGCATCGCTGGTCATACGCGAACACGTACCAACAGCAATGGTGAGGCGGCATCAAGAGCAGGGATCCGTCATTTATCCGAGCATTTTACCCCAAAAACCTTTTATTTATAAGGGTCATTGCGAATTATCTGATGCAAAGTTATGTTATGTTAGGCAAAGTAATCTTCTATTATTAATAAGCACATCAAAACCTTTTTGAATATTAAATAATAATTAATTAGCATCATCCTCATTCATTAATTCCGCTTAACAATAGTTTCACACCTTGCCCCCATTGCGACACCTCGGAAATCATCACGCAGTTAAACTCTCCGTAATGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTA  >  NC_000913/2406935‑2407422

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.