New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1397238	NA (NA)	32 (0.880)	30/488	0.3	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	= 1978494	0 (0.000)					intergenic (‑297/+24)	flhD/insB5	DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB

ACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACG  >  NC_000913/1978245‑1978740                                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                       cccccgtgaaggagCCGGGAAGTCCCGGTAAAAAAAAATTAGAAGTAGAAGAGGTGCGATAAGCTGCAATAAGCAGAAACACCTTATTGGTTTAATATGTCCTTACAAATAGAAAAGGGTCTTTACCCTTATCTAAGATTTTTCCTAAAACGACGCAACAGTACTCGTCACTAAACGCACAGACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCTGATCACACAAAACACTCAATTACATaag                                                                                                                                                                                                                                                       <  2:391434/238‑2 (MQ=255)        gatgtagcaaagaggCCCCGGACAAAAATAATTAGCCTTAGAATAGATGCGATCCGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGACATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCACCTGTACTCGTCACTACACGCAACTCCACCGGAGGGGG‑CTGCGATTTTCCATAATGAGTGATGCAACTCACAAAAAAAACTCAATTACTTaaggaaggtgc                                                                                                                                                                                                                                               >  2:244325/15‑242 (MQ=255)        gATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtg                                                                                                                                                                                                                                                >  1:344174‑M2/1‑243 (MQ=255)         aTGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgc                                                                                                                                                                                                                                               >  1:224203‑M2/1‑242 (MQ=255)                cGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACCAAACACTCAATTACTTAAggaaggtgcgaata                                                                                                                                                                                                                                          <  2:304989‑M2/249‑15 (MQ=255)                  ggAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcg                                                                                                                                                                                                                                      <  1:274849‑M2/251‑19 (MQ=255)                  ggAAGACCCGGTAAAAAATAATTAGCATTATAATAGTTGCGATAAGCTGCACTAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAACTGTGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACACCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAgtaaggtgcgaataagcg                                                                                                                                                                                                                                      <  1:211750‑M2/251‑19 (MQ=255)                   gAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTACGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATACTGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggggcgaataagcgg                                                                                                                                                                                                                                     <  1:427649‑M2/251‑20 (MQ=255)                     aGCCACGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcgggg                                                                                                                                                                                                                                   <  1:270881‑M2/251‑22 (MQ=255)                              aaaaaaTAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttc                                                                                                                                                                                                                          >  1:196002‑M2/1‑221 (MQ=255)                               aaaaaTAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCTCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAACACACTAAATTACTTAAggaatgtaagaataagcggggaacttcttct                                                                                                                                                                                                                         <  2:130655‑M2/251‑32 (MQ=255)                                                gAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatt                                                                                                                                                                                                        <  1:403267‑M2/251‑49 (MQ=255)                                                          gATAAGCTGAAATAAGCAGAACCATCTTTTTTGTTTAATATGTCCTTACAAATTGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaatgttcgaataagcggggaaagtcttctcggctgactcagtcatttcatttcttc                                                                                                                                                                                              >  2:288039‑M2/1‑193 (MQ=255)                                                           aTAAGCTTCAATAAGCAGAACCACCTTTTTTGTTTTATATATCCTTACAAATATAAATGGGTCTTTACACTTATCTAAGAATTTTCCTAAAGCGACGTAACTGTACTCGTCACTTCACGCACATACAACGGAGGGTGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggacggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttca                                                                                                                                                                                             >  2:371968‑M2/1‑192 (MQ=255)                                                                     aTAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagcc                                                                                                                                                                                   <  1:405044‑M2/251‑70 (MQ=255)                                                                        aGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttctgcatgtttgagccgat                                                                                                                                                                                >  1:337599‑M2/1‑179 (MQ=255)                                                                          cAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattt                                                                                                                                                                              >  1:229141‑M2/1‑177 (MQ=255)                                                                                     ttttGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccg                                                                                                                                                                     >  1:42980‑M2/1‑166 (MQ=255)                                                                                      tttGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAAAGCGTGATGCAGATCACACAAAACACTCAATTACTTACggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgta                                                                                                                                                                   <  2:219116‑M2/250‑86 (MQ=255)                                                                                         ggTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGAACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagaggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcacgtaaatg                                                                                                                                                               <  1:154467‑M2/251‑90 (MQ=255)                                                                                              aagttgtccTTACAAAAAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGTCGCAACTGTACTCGTCACGACACGCACATACAACGGAGGGGGGCTGCGTTTTTCAATAATGCGTGATGCAGATCACATAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccgt                                                                                                                                                           >  2:214962‑M2/5‑157 (MQ=255)                                                                                                 atGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaa                                                                                                                                                                 >  1:433806‑M2/1‑154 (MQ=255)                                                                                                 atGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTAGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaa                                                                                                                                                                 <  2:433806‑M2/241‑88 (MQ=255)                                                                                                       ttACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcct                                                                                                                                                 <  1:393163‑M2/251‑104 (MQ=255)                                                                                                               aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagac                                                                                                                                         >  1:225627‑M2/1‑140 (MQ=255)                                                                                                                         cTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCATCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctggctcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcatcctatttagaccgtttcttcg                                                                                                                               <  2:117418‑M2/251‑122 (MQ=255)                                                                                                                                      tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagaccgtttcttcgccatttaaggcgt                                                                                                                  <  1:47211‑M2/251‑135 (MQ=255)                                                                                                                                       aaGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagaccgtttcttcgccatttaaggc                                                                                                                    >  1:304989‑M2/1‑116 (MQ=255)                                                                                                                                             tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagaccgtttcttcgccatttaaggcgttatccc                                                                                                            >  1:198265‑M2/1‑110 (MQ=255)                                                                                                                                                     aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagaccgtttcttcgccatttaaggcgttatccccagttttt                                                                                                    <  1:58665‑M2/250‑149 (MQ=255)                                                                                                                                                                 gTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagaccgtttcttcgccatttaaggcgttatccccagtttttagtgagatctctc                                                                                       <  1:53520‑M2/251‑162 (MQ=255)                                                                                                                                                                                                     cTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagaccgtttcttcgccatttaaggcgttatccccagtttttagtgagatctctcccactgacgtatcatttggtccgcccgaaacaggtt                                                   <  1:41139‑M2/251‑198 (MQ=255)                                                                                                                                                                                                                                       caAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagaccgtttcttcgccatttaaggcgttatccccagtttttagtgagatctctcccactgacgtatcatttggtccgcccgaaacaggttggccagcgtgaataacatcgccagttggttatcg                 <  1:114051‑M2/251‑232 (MQ=255)                                                                                                                                                                                                                                                      cTTAAggacggtgcgaataagcggggaaattcttctcggcagactccgtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagaccgtttcttcgccatttaaggcgttatccccagtttttagtgagatctctcccactgacgtataatttggtccgcccgaaaaaggttggcccgcgtgactaacatcgccagttggttatcgtttttcagcaacccc  <  2:36411‑M2/251‑247 (MQ=255)                                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                       ACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACG  >  NC_000913/1978245‑1978740

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.