New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 3948058	36 (0.740)	3 (0.070)	3/244	NT	7.4%	intergenic (‑10/+51)	PP_3483/PP_3484	type II secretion system protein/two‑component system response regulator
	?	NC_002947	= 3948073	42 (0.920)					intergenic (‑25/+36)	PP_3483/PP_3484	type II secretion system protein/two‑component system response regulator

GGCATGCCCGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAACACCCAGCTTCCATCGTACAACT  >  NC_002947/3947921‑3948203                                                                                                                                          |                                                                                                                                                    ggCATGCCCGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAggg                                                                                                                                          <  1:213000/149‑1 (MQ=255)        ccGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCGTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAgggagcacc                                                                                                                                    >  7:206080/1‑142 (MQ=255)              ccACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCgtcgcaggc                                                                                                                             <  7:203886‑M2/149‑10 (MQ=255)                        aTCACAGGTCTGTGGGCTGCATTCATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCATGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGc                                                                                                                    <  8:79683/148‑1 (MQ=255)                         tCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGc                                                                                                                    >  6:243406/1‑147 (MQ=255)                               gTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACGCGCCCCTGAGCGGAgtcgcaggccatgccagaagctgg                                                                                                              <  2:61140‑M2/147‑25 (MQ=255)                                          gCATACATCCTGTGGTAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGcgccgc                                                                                                >  7:104812/1‑148 (MQ=255)                                          gCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGcgccgc                                                                                                >  4:270279/1‑148 (MQ=255)                                            aTACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTACGGGGTTGCATCGCATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGATCGGCCA‑G‑GGGTGCGGGCGCAGCTAt                                                                                             >  5:213752/1‑149 (MQ=255)                                                aTCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCgtcgca                                                                                                                                >  6:163407‑M2/1‑106 (MQ=255)                                                aTCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCgtcgca                                                                                                                                <  5:163407‑M2/112‑7 (MQ=255)                                                  ccTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCt                                                                                       >  4:162064/1‑149 (MQ=255)                                                      tgGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCtgt                                                                                     >  4:144691/1‑147 (MQ=255)                                                       gggAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑GCGGGTGCGGGCGCCGCTATTCCCCTGTGa                                                                                   <  1:175061/149‑1 (MQ=255)                                                          aGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAg                                                                               >  7:69911/1‑149 (MQ=255)                                                            cGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGt                                                                              <  8:104812/148‑1 (MQ=255)                                                                   gCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCt                                                                                       >  2:274696/1‑132 (MQ=255)                                                                   gCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCt                                                                                       <  1:274696/132‑1 (MQ=255)                                                                     ccGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGAtcgtcgt                                                                    >  5:303285/1‑149 (MQ=255)                                                                         gAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACgcgcccctgagcggagtcgca                                                                                                                                <  4:6749‑M1/87‑22 (MQ=255)                                                                         gAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACgcgcccctgagcggagtcgca                                                                                                                                >  3:6749‑M1/1‑66 (MQ=255)                                                                         gAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCggg                                                                <  3:270279/149‑1 (MQ=255)                                                                                 cGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCtggtg                                                        >  4:45736/1‑149 (MQ=255)                                                                                              gCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGAtcgtcgt                                                                    <  1:13994/124‑1 (MQ=255)                                                                                              gCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGt                                            >  7:160362/1‑148 (MQ=255)                                                                                              gCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTCGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGAtcgtcgt                                                                    >  2:13994/1‑124 (MQ=255)                                                                                               cAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGtt                                           <  3:144691/148‑1 (MQ=255)                                                                                                aGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTAc                                         <  6:303285/149‑1 (MQ=255)                                                                                                      cGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTAcggcgg                                    <  8:69911/148‑1 (MQ=255)                                                                                                       ggggTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTAcggcggcg                                  >  2:59733/1‑149 (MQ=255)                                                                                                              cATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGcc                           <  8:160362/149‑1 (MQ=255)                                                                                                                 cGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCaa                         >  5:313649/1‑148 (MQ=255)                                                                                                                   ccagcttCTGGCATGGCCTGCGACtccgctcaggggcgcgtcgcaggccatgccagaagcattcgatgcaaccccggaatctgcaaagcctgcaccgacgtcttcgcgggcatgcccgctcccacaggatgtatgcagcccacagac                          <  2:61140‑M1/144‑124 (MQ=255)                                                                                                                    aTGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGG‑GGGTGCGGGAGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAacac                      >  1:242575/1‑149 (MQ=255)                                                                                                                    aTGCTTATGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGTGGCGGTCGGCCAACAcc                     <  8:203886/149‑1 (MQ=255)                                                                                                                       cttattgCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCTTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAACACCCAg                  <  6:213752/143‑1 (MQ=255)                                                                                                                              cATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAACACCCAGCTTCCAt           >  5:309137/1‑149 (MQ=255)                                                                                                                               aTGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAACACCCAGCTTCCATc          <  3:45736/149‑1 (MQ=255)                                                                                                                                  gCCTGCGACgcgcccctgagcggagtcgcaggccatgccagaagcattcgatgcaaccccggaatctgcaaagcctgcaccgacgtcttcgcgggcatgcccgctcccacaggatgtatgcagcccacagacctgtgatgtacctgtgg         <  7:203886‑M1/149‑141 (MQ=255)                                                                                                                                   ccTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGAtc                                                                         >  2:135573/1‑82 (MQ=255)                                                                                                                                   ccTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGAtc                                                                         <  1:135573/82‑1 (MQ=255)                                                                                                                                   ccTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAACACCCAGCTTCCATCGTAc      <  4:106843/149‑1 (MQ=255)                                                                                                                                    cTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAACACCCAGCTTCCATCGTAc      >  4:297772/1‑148 (MQ=255)                                                                                                                                    cTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAACACCCAGCTTCCATCGTAc      >  4:302389/1‑148 (MQ=255)                                                                                                                                     tGCGACgcgcccctgagcggagtcgcaggccatgccagaagcattcgatgcaaccccggaatctgcaaagcctgcaccgacgtcttcgcgggcatgcccgctcccacaggat                                           >  6:163407‑M1/1‑6 (MQ=255)                                                                                                                                     tGCGACgcgcccctgagcggagtcgcaggccatgccagaagcattcgatgcaaccccggaatctgcaaagcctgcaccgacgtcttcgcgggcatgcccgctcccacaggat                                           <  5:163407‑M1/112‑107 (MQ=255)                                                                                                                                     tGCGACTCCGCTCAGGGGCGCgtcgcaggccatgccagaagcattcgatgcaaccccggaatctgcaaagcctgcaccgacgtcttc                                                                    >  3:6749‑M2/1‑21 (MQ=255)                                                                                                                                     tGCGACTCCGCTCAGGGGCGCgtcgcaggccatgccagaagcattcgatgcaaccccggaatctgcaaagcctgcaccgacgtcttc                                                                    <  4:6749‑M2/87‑67 (MQ=255)                                                                                                                                       cGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAACACCCAGCTTCCATCGTACAACt  <  5:197973/149‑1 (MQ=255)                                                                                                                                          |                                                                                                                                                    GGCATGCCCGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCA‑G‑GGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGTCGGGCCCTGGTGGCTTGGCGCCGTTACGGCGGCGGTCGGCCAACACCCAGCTTCCATCGTACAACT  >  NC_002947/3947921‑3948203

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.