New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1397325	NA (NA)	34 (0.670)	32/482	0.5	100%	intergenic (+233/‑40)	insH4/ynaJ	IS5 family transposase and trans‑activator/DUF2534 domain‑containing protein YnaJ
	?	NC_000913	1427513 =	0 (0.000)					pseudogene (125/210 nt)	lomR	Rac prophage; protein LomR_1

GAATGTCGGCAAAACAAACGGCTTTTGCTATGCGCATGTTGCCTGCACAAATGACGGATATTGTTGTTGGGTTGTCCACTGGTCAGTCGCCATTTATGGTGTTAATGCAGCAGGGCGGCCATTCAGCTATGCAGGAGACAAGAATCGCCAGCTTACCCGTTACAGCGATACCCGCTGGCATGAAGATTCCGTGCGTAACCGCTGGTTCAGCGTGATGGTGGGGCCGTCTGTGCGCGTGAATGAATGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTATTTTTTCCACCATTTCTGGCGTTATTTCCGGTTTTTACTGAGA  >  NC_000913/1427268‑1427754                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                  agatctcactaaaaactggggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagactttccccgcttattcgcaccttccctcactaatcaatgcgttgattgtaaatccagctaagaggtgcggttttcagagcagacaacggtgaaatgacatggtattgttacgGGTTc                                                                                                                                                                                                                                               >  2:320976‑M2/246‑250 (MQ=255)       cactaaaaactggggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcgctaacgaatcaatgcgttgattggaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAgc                                                                                                                                                                                                                                            <  2:307718‑M2/8‑1 (MQ=255)           aaaaactggtgataacgccttaaatggcgaagaaacggtctaaataggctgattcaagtcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgcctgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctatgagttgaggttttcagagtagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTAt                                                                                                                                                                                                                                      <  2:295464‑M2/14‑1 (MQ=255)                    ggataacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCggg                                                                                                                                                                                                                           >  1:26714‑M2/227‑251 (MQ=255)                       taacgccttaaatggcgaagaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTAt                                                                                                                                                                                                                        >  1:10165‑M2/224‑251 (MQ=255)                                         agaaacggtctaaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTc                                                                                                                                                                                                      <  1:2263‑M2/46‑1 (MQ=255)                                                    aaataggctgattcaaggcattttcgggagaaaaaatcggcacaaacaggaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaagccagctaagaggtgaggttttcagagcagacaacggtgaaatttcatggtattgttacgGGTTCAGCGCGTATGCGATGGCTGTTATGGCTTACAGCCGTGTGTCGActttcgcc                                                                                                                                                                                            <  2:34378‑M2/56‑4 (MQ=255)                                                    aaataggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTtct                                                                                                                                                                                              <  1:530200‑M2/54‑1 (MQ=255)                                                       taggctgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCgggg                                                                                                                                                                                        >  1:440903‑M2/192‑251 (MQ=255)                                                            tgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCg                                                                                                                                                                                                            <  2:278934‑M2/40‑1 (MQ=255)                                                            tgattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCg                                                                                                                                                                                                            >  1:278934‑M2/187‑226 (MQ=255)                                                             gattcaaggcatttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaattgccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacatcggtgaaatggcatggtattgttacgGGTTCAGCGCGTATGCGATTGCGGGTATGGCTTACAGCCGTGTGTCGCCTTTCTCCGGGGATTAt                                                                                                                                                                                   <  2:449570‑M2/65‑1 (MQ=255)                                                                       atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAAc                                                                                                                                                                        >  1:238103‑M2/176‑251 (MQ=255)                                                                                 gaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttcttcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagcggtgaggttttcagagcagacaaaggtgaaatgtcatggaattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACCGCCGTGTGTCGAACTTCTCCGGGGATTATCCCCGCGTAACTGacaaca                                                                                                                                                                >  2:257912‑M2/166‑249 (MQ=255)                                                                                                          aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCAtt                                                                                                                                     <  2:98464‑M2/111‑1 (MQ=255)                                                                                                                            gccgagaagaatttccccgcttattcgcaccgtccctaactaatcaatgcgttgattgtaaatccagcgaagaggtgaggttttcagagcagacaacggtgaaatgtcagggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCg                                                                                                                   <  2:163324‑M2/129‑1 (MQ=255)                                                                                                                                                     cgcaccttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTggg                                                                                          >  1:39006‑M2/98‑251 (MQ=255)                                                                                                                                                          cttccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGAt                                                                                     >  1:192604‑M2/93‑251 (MQ=255)                                                                                                                                                            tccctaactaagcaatgcgttgattgtaaatccagctaagaggtgaggttgtcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGCCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGAt                                                                                     <  2:440903‑M2/159‑1 (MQ=255)                                                                                                                                                             ccctaactaatcaatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGAtttt                                                                                  >  1:508597‑M2/90‑251 (MQ=255)                                                                                                                                                                        caatgcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGACGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGCTTTTTTTCCCGCaa                                                                        >  2:203158‑M2/79‑250 (MQ=255)                                                                                                                                                                            gcgttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAAcaca                                                                   <  1:320976‑M2/177‑1 (MQ=255)                                                                                                                                                                              gttgattgtaaatccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATc                                                                 <  2:10165‑M2/179‑1 (MQ=255)                                                                                                                                                                                       aaatccagctaagaggtgaggttttcagagcagacaacggtgaaaagtcgtggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTACCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGcc                                                        <  2:278159‑M2/188‑1 (MQ=255)                                                                                                                                                                                           ccagctaagaggtgaggttttcagagcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCCAACACATCGAATCAGCCTAtt                                                    >  2:107080‑M2/60‑251 (MQ=255)                                                                                                                                                                                                                    gcagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTACCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTATTTTTTCCACCATTTCTg                           <  1:13010‑M2/217‑1 (MQ=255)                                                                                                                                                                                                                     cagacaacggtgaaatgtcatggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTAGGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATGTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTATTTTTTCCACCATTTCTgg                          <  2:238103‑M2/218‑1 (MQ=255)                                                                                                                                                                                                                                  aatgtcatggtattgttacgGGTTCAGCGCGTCTGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACACGGGAAGGTGCGCATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTATTTTTTCCACCATTTCTGGCGTTATTTCCGGt             >  1:530823‑M2/21‑251 (MQ=255)                                                                                                                                                                                                                                   aggtcatggtattgtgacgggTTCAGCGCGTATGCGAGGGCGGGTATGGCTTACAGCGGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCGGATTAAAAGTTCGCGGATCTGGGCCTAGTTTTTTCCCGCTAACACATCTAATCAGCCTAGGGAGTTTATGTTGTCCACCAGATCTGGCGTTATGTCCGGtt            <  2:530823/232‑1 (MQ=255)                                                                                                                                                                                                                                        atggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTCTGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTATTTTTTCCACCATTTCTGGCGTTAttt                  >  1:240973‑M2/15‑240 (MQ=255)                                                                                                                                                                                                                                        atggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTAttt                                          >  1:440362‑M2/15‑216 (MQ=255)                                                                                                                                                                                                                                        atggtattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTAttt                                          <  2:440362‑M2/202‑1 (MQ=255)                                                                                                                                                                                                                                        atggtattgttacgGGTCCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTATTTTTTCCACCATTTCTGGCGTTAttt                  <  2:240973‑M2/226‑1 (MQ=255)                                                                                                                                                                                                                                          gttattgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTATTTTTTCCACCATTTCTGGCGTTATTTCCGGTTTTTACt      <  2:26714‑M2/238‑1 (MQ=255)                                                                                                                                                                                                                                             attgttacgGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTATTTTTTCCACCATTTCTGGCGTTATTTCCGGTTTTTACTgaga  <  1:257912‑M2/242‑1 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                  GAATGTCGGCAAAACAAACGGCTTTTGCTATGCGCATGTTGCCTGCACAAATGACGGATATTGTTGTTGGGTTGTCCACTGGTCAGTCGCCATTTATGGTGTTAATGCAGCAGGGCGGCCATTCAGCTATGCAGGAGACAAGAATCGCCAGCTTACCCGTTACAGCGATACCCGCTGGCATGAAGATTCCGTGCGTAACCGCTGGTTCAGCGTGATGGTGGGGCCGTCTGTGCGCGTGAATGAATGGTTCAGCGCGTATGCGATGGCGGGTATGGCTTACAGCCGTGTGTCGACTTTCTCCGGGGATTATCTCCGCGTAACTGACAACAAGGGAAGGTGCGAATAAGCAGGTCATTTCTTCCCAAGCTGACTCGCTGATTAAAATTTCGCGGATCTGGGCCGATTTTTTTCCCGCAAACACATCGAATCAGCCTATTTAGGCTATTTTTTCCACCATTTCTGGCGTTATTTCCGGTTTTTACTGAGA  >  NC_000913/1427268‑1427754

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ 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.