New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3110452	43 (0.950)	4 (0.090)	3/260	NT	8.8%	intergenic (+11/+138)	pheV/yghD	tRNA‑Phe/putative type II secretion system M‑type protein
	?	NC_000913	= 3110475	41 (0.920)					intergenic (+34/+115)	pheV/yghD	tRNA‑Phe/putative type II secretion system M‑type protein

TGAAGAAATTTGATTGACGAGACGAGGCGAATCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTT  >  NC_000913/3110314‑3110591                                                                                                                                           |                                                                                                                                            tGAAGAAATTTGATTGACGAGACGAGGCGAATCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCGCTAATTCTTAAGAAc                                                                                                                                         >  1:493839/1‑143 (MQ=255)   aagaaATTTGATTGACGAGACGAGGCGAATCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAAccc                                                                                                                                       >  2:571858/1‑143 (MQ=255)      gaaTTTGATTGACGAGACGAGGCGAATCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGcc                                                                                                                                    <  1:776960/142‑1 (MQ=255)         tttGATTGACGAGACGAGGCGAATCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCCCTACTGCTTAAaaacccgccccc                                                                                                                                 >  1:394531‑M1/1‑131 (MQ=255)         tttGATTGACGAGACGAGGCGAATCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCcac                                                                                                                                 >  1:6549/1‑143 (MQ=255)         tttGATTGACGAGACGAGGCGAATCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCcac                                                                                                                                 <  1:521263/143‑1 (MQ=255)                        gagGCTAAGCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGATCCCGCCCACAAGGCGGGTTTTTGc                                                                                                                  <  1:852472/143‑1 (MQ=255)                          ggCGAATCATGTTTAGTGCGCGCCGTTGCCCGGATAGTTCAGTCGGTAGAGTAGGGTATTGAGATTCCCCGGGTCATTGGTTCGATTAAGAGGCCGGGCACCACTAATTCTTAAaaacccgccttgtgggcgggttcttaaga                                                                                                                <  1:624169‑M1/143‑30 (MQ=255)                                tCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCttt                                                                                                               <  1:663671/138‑1 (MQ=255)                                tCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCttt                                                                                                               >  2:663671/1‑138 (MQ=255)                                  aGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTCGATCt                                                                                                        >  2:65455/1‑143 (MQ=255)                                    ggttAATGCGGCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGa                                                                                                      <  2:265991/141‑1 (MQ=255)                                    gTTTAATGCGCTCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGa                                                                                                      <  1:864386/143‑1 (MQ=255)                                    gTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAGATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGCTCCTGCGTTTGGATCTGa                                                                                                      >  2:580943/1‑143 (MQ=18)                                    gTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTCAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGa                                                                                                      >  1:604756/1‑143 (MQ=255)                                     tttAATGCGCCCCGTTGCGCGGATAGCGCAGTCGGTAGAGCAGGGGGTTGAAAATCGCCGTGTCCTTGGTTCGATTCCGAGTCGGGGCACCACTAATTCTTAAGACCCCGCCCACACGGCGGGTTTTTGCTTTTGGATCTGAc                                                                                                     >  2:520256/1‑143 (MQ=21)                                        aaTGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACact                                                                                                  >  1:800366/1‑141 (MQ=255)                                          gtccgcccGTCGCCCTCATAGCTCAGTCGGTAGAGCAGGGGATTGAAAACCCCCGTGTCCGTGGTTCGACGCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATaa                                                                                                <  2:26944/138‑1 (MQ=25)                                              ccccGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGCTCTGACAATAACCtt                                                                                            >  1:314707/1‑143 (MQ=255)                                                ccGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGCCAATCACCTTCa                                                                                          >  1:703064/1‑143 (MQ=255)                                                 cGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCAc                                                                                         <  2:783571/143‑1 (MQ=255)                                                             aGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAg                                                                             <  1:394568/143‑1 (MQ=255)                                                             aGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAg                                                                             <  1:123136/143‑1 (MQ=255)                                                              gcgcAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGc                                                                            <  1:787581/140‑1 (MQ=255)                                                               cTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCCCCACTAAGTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATCACCTTAACGAAAACAATTAGCt                                                                           >  1:141169/1‑143 (MQ=25)                                                                       gTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAGCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGt                                                                   <  2:576577/143‑1 (MQ=255)                                                                            gCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCCCGAAAAAAATTAGCTTATAAAGTCTggg                                                              >  2:851151/1‑143 (MQ=255)                                                                             cAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAaaacccgccttgtgggcgggttcttaaga                                                                                                                <  2:272076‑M1/92‑30 (MQ=255)                                                                             cAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAaaacccgccttgtgggcgggttcttaaga                                                                                                                >  1:272076‑M1/1‑63 (MQ=255)                                                                             cAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTgggg                                                             >  1:490179/1‑143 (MQ=255)                                                                               ggggATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGa                                                           <  1:819735/143‑1 (MQ=255)                                                                                          aTCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc                                                <  1:571858/143‑1 (MQ=255)                                                                                                  gtCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACTTTac                                        >  1:381566/1‑142 (MQ=255)                                                                                                   tCCTGGGTTCGATTCCGAGCCCGGGCACCACTAATTCTTAAGACCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAAc                                       <  1:671297/143‑1 (MQ=255)                                                                                                      ttGGTTCGATTCCGAGTCCGGGCACCCCTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGAAACTGCTGGGCGCGAGTGAAATTAGCTTATCAAGTCTGGGGGAATTACTCTCGCCACGTTAACgag                                    >  1:888389/1‑143 (MQ=255)                                                                                                      ttGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGTGTTGTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTGGCCACGTTAACgag                                    >  1:82358/1‑143 (MQ=255)                                                                                                      ttGGTTCGATTCCGAGGCAGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTGTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATAAGCTTATAAAGACTGGGGGAATTCCCCTCGGCACGTTACCgag                                    >  2:503123/1‑143 (MQ=255)                                                                                                       tGGTGCGACCCCTAGCCCGGGCACGACTAATGCGTAAGAACCCCCCCACAAGGCGGGTTGTTGCTGTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACgaga                                   <  1:365857/143‑1 (MQ=255)                                                                                                       tGGATCGATCCCGAGTCCGGGCACCACTAATTCTGAAGAACCCGCCCAGAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAACTAGCCTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACgaga                                   <  2:895894/143‑1 (MQ=255)                                                                                                          ttCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAACAATTAGCTTATACAGTCTGGGGGAATTACTCTCGCCACGTTAACgacggga                                >  1:71850/1‑138 (MQ=255)                                                                                                                         gggCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTa                 >  1:858336/1‑143 (MQ=255)                                                                                                                         gggCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTACACGAACAAAATTAGCTTATAAAGTCTGGGGGAATTACACACGCCACGTTAACGAGAGTAATTTTATTGatctca                 >  2:197531/1‑139 (MQ=255)                                                                                                                             accacTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATGAGGTCTGGGGGAATTACTCGCGCCACGTTAACGAGAGTAATTTTATTGATACTAAtct             >  2:127111/1‑143 (MQ=255)                                                                                                                               cacTAATTCTTAAGACCCCCCCGACTTGGTGTTTTGCAGCTAGTGTATCTGACAATAACCTTCACAAAACAAATTAGCTTATAAAGTCTGGGGGTGTTTCTCTCGCCACGCTAACGAGCGAAATTTTATTGAGATTAATCTcc           >  2:401633/1‑143 (MQ=255)                                                                                                                                 cTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTg         >  1:823970/1‑143 (MQ=255)                                                                                                                                  tAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTGTATTAAGATTAATCTCCGGa        >  2:713641/1‑143 (MQ=255)                                                                                                                                     ttCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATATTATTGATATTAATCTCCTGATAc     >  1:805978/1‑143 (MQ=255)                                                                                                                                      tCTTAAGAACCCGCCCACAAGGCGGGTTTttaagaattagtggtgcccggcctcttaatcgaaccaatgacccggggaatctcaataccctactctaccgactgaactatccgggcaacggcgcgcactaaacatgattcgcc    <  1:624169‑M2/143‑115 (MQ=255)                                                                                                                                      tCTTAAGAACCCGCCCACAAGGCGGGTTTttaagaattagtggtgcccggactcggaatcgaaccaaggacacggggattttcaatcccctg                                                       <  2:272076‑M2/92‑64 (MQ=255)                                                                                                                                      tCTTAAGAACCCGCCCACAAGGCGGGTTTttaagaattagtggtgcccggactcggaatcgaaccaaggacacggggattttcaatcccctg                                                       >  1:272076‑M2/1‑29 (MQ=255)                                                                                                                                      tCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGACAAAAATTAGCTTATAAAGTCTGGGGGCATTACTCTCGCCACGTTAACGAGAGTACTTTTATGAATATTAATCCCCTgttcct    >  2:721864/1‑138 (MQ=255)                                                                                                                                        ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACttt  >  1:87992/1‑143 (MQ=255)                                                                                                                                           |                                                                                                                                            TGAAGAAATTTGATTGACGAGACGAGGCGAATCAGGTTTAATGCGCCCCGTTGCCCGGATAGCTCAGTCGGTAGAGCAGGGGATTGAAAATCCCCGTGTCCTTGGTTCGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTT  >  NC_000913/3110314‑3110591

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ 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.