New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	5608540 =	51 (0.970)	4 (0.080)	4/242	NT	8.2%	coding (1058/1272 nt)	waaA	3‑deoxy‑D‑manno‑octulosonic acid transferase
	?	NC_002947	5608576 =	41 (0.810)					coding (1022/1272 nt)	waaA	3‑deoxy‑D‑manno‑octulosonic acid transferase

CAGTTCCACCAGGCGGCGCACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTCGCCCATGGTGTCGCCCAGCAATACCCGCGTTTGCGCATCGACCAGCGTGCCGG  >  NC_002947/5608431‑5608714                                                                                                                                                  |                                                                                                                                           cAGTTCCACCAGGCGGCGCACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCt                                                                                                                                         >  8:113996/1‑149 (MQ=255)  aGTTCCACCAGGCGGCGCACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGc                                                                                                                                          >  1:221627/1‑147 (MQ=255)  aGTTCCACCAGGCGGCGCACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGc                                                                                                                                          <  2:221627/147‑1 (MQ=255)      ccaccaGGCGGCGCACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCaa                                                                                                                                     <  7:113996/148‑1 (MQ=255)       caccaGGCGGCGCACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAACATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAAc                                                                                                                                    <  6:309583/148‑1 (MQ=255)         ccaGGCGGCGCACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGa                                                                                                                                 >  5:93747/1‑149 (MQ=255)                gcgcACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGcc                                                                                                                          >  7:300533/1‑149 (MQ=255)                   cACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTGGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCGAGCGCCGCAGGCTCCAACGGATTGTGCCCAc                                                                                                                       >  8:67611/1‑149 (MQ=255)                    aCCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCAcc                                                                                                                      <  6:93747/149‑1 (MQ=255)                                aGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCTGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAg                                                                                                          >  4:62452/1‑149 (MQ=255)                                     gTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCTGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGc                                                                                                     <  3:62452/149‑1 (MQ=255)                                          catcatCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCAcc                                                                                                 >  3:46811/1‑148 (MQ=255)                                          catcatCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCAcc                                                                                                 >  8:255172/1‑148 (MQ=255)                                              atcCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACcgacg                                                                                             >  8:43463/1‑148 (MQ=255)                                               tcCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGaa                                                                                           <  6:198822/149‑1 (MQ=255)                                                 cACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAgg                                                                                         >  5:360632/1‑149 (MQ=255)                                                    ctgctgCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCaa                                                                                      <  6:360632/149‑1 (MQ=255)                                                       ctgcAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACAGATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAAt                                                                                     <  4:314609/147‑1 (MQ=255)                                                       ctgcAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAAt                                                                                     <  4:46811/147‑1 (MQ=255)                                                          cAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCgg                                                                                                                >  7:5442/1‑117 (MQ=255)                                                          cAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCgg                                                                                                                <  8:5442/117‑1 (MQ=255)                                                          cAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCg                                                                                 <  7:255172/148‑1 (MQ=255)                                                            ttcgtcggtggcagcctggtgccgaccggtgggcacaatccgttggagccTGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAg                                                                                                                                            <  5:183058‑M1/37‑1 (MQ=255)                                                            ttcgtcggtggcagcctggtgccgaccggtgggcacaatccgttggagccTGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAg                                                                                                                                            >  6:183058‑M1/51‑87 (MQ=255)                                                               cccccGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAgg                                                                           >  7:296822/1‑149 (MQ=255)                                                                   cGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCAt                                                                       <  7:43463/149‑1 (MQ=255)                                                                    gCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATa                                                                      >  1:99605/1‑149 (MQ=255)                                                                     ccTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATa                                                                      >  6:176381/1‑148 (MQ=255)                                                                                aTCGCGCTGATTTCGAGGAAGTTGAAAACATGCGGCCCCATGCTCACCGGCAATGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAAcagcag                                                          <  6:360324/149‑1 (MQ=255)                                                                                 tCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATATAGGAACAGCAGt                                                         <  8:296822/149‑1 (MQ=255)                                                                                 tCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGACAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGt                                                         >  5:141539/1‑149 (MQ=255)                                                                                     gcTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACGGGAACAGCAGTTCGc                                                     <  8:300533/149‑1 (MQ=255)                                                                                      cTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCTGTCGGCACCAGGCTGc                                                                                                     <  8:176807/100‑1 (MQ=255)                                                                                      cTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGc                                                                                                     >  7:176807/1‑100 (MQ=255)                                                                                         aTTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTCGCCCAt                                                 <  5:176381/149‑1 (MQ=255)                                                                                              gAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAg                                                                                          <  4:92961/103‑1 (MQ=255)                                                                                                ggAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAAcagc                                                            <  1:258603/131‑1 (MQ=255)                                                                                                ggAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAAcagc                                                            >  2:258603/1‑131 (MQ=255)                                                                                                        aaCACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAggg                                                                          >  6:240096/1‑109 (MQ=255)                                                                                                        aaCACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAggg                                                                          <  5:240096/109‑1 (MQ=255)                                                                                                         ccacaTGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGACAATGTCGGCCAGGGCATACAGGAAcagca                                                           <  4:302717/122‑1 (MQ=255)                                                                                                         acacATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTCGCCCATGGTGTCGCCCAg                                     >  6:173347/1‑145 (MQ=255)                                                                                                         acacATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTCGCCCATGGTGTCGCCCAg                                     <  5:173347/145‑1 (MQ=255)                                                                                                             ctgcggcgctggccttgccggtgctcatggggccgcaGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGaa                                                                                           >  6:183058‑M2/38‑87 (MQ=255)                                                                                                             ctgcggcgctggccttgccggtgctcatggggccgcaGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGaa                                                                                           <  5:183058‑M2/50‑1 (MQ=255)                                                                                                              tgcggcgctggccttgccggtgctcatggggccgcaGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCa                                                                             >  8:197575‑M2/37‑100 (MQ=255)                                                                                                              tgcggcgctggccttgccggtgctcatggggccgcaGGCTCCAACGGATTGTGCCCACCGGGCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCa                                                                             <  7:197575‑M2/64‑1 (MQ=255)                                                                                                                  GCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTc                                                       <  3:206090‑M1/118‑1 (MQ=255)                                                                                                                  GCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTc                                                       >  4:206090‑M1/1‑118 (MQ=255)                                                                                                                            cACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTCGCCCATGGTGTCGCCCAGCAATACCCGCGTTTGCGCATCGa              >  2:303082/1‑149 (MQ=255)                                                                                                                             aCCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTCGCCCATGGTGTCGCCCAGCAATACCCGCGTTTGCGCATCGAc             <  1:303082/149‑1 (MQ=255)                                                                                                                                   aaGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTCGCCCATGGTGTCGCCCAGCAATACCCGCGTTTGCGCATCGACCAGCGt       >  7:16218/1‑149 (MQ=255)                                                                                                                                        cAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCCCCGACGCAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTCGCCCATGGGGTCGCCCAGCAATACCCGCGTTTGCGCATCGACCAGCGTGCCgg  >  7:182774/1‑149 (MQ=255)                                                                                                                                        cAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACcgacga                                                                                            <  6:114526/59‑1 (MQ=255)                                                                                                                                        cAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACcgacga                                                                                            >  5:114526/1‑59 (MQ=255)                                                                                                                                                  |                                                                                                                                           CAGTTCCACCAGGCGGCGCACCGCGCCGGCCAGCCCGTCAGCATCATCCACCTGCTGCAACGCCCCCGCCTCGCGCAGCATCGCGCTGATTTCGAGGAAGTTGAACACATGCGGCCCCATGAGCACCGGCAAGGCCAGCGCCGCAGGCTCCAACGGATTGTGCCCACCGGTCGGCACCAGGCTGCCACCGACGAAGGCAATGTCGGCCAGGGCATACAGGAACAGCAGTTCGCCCATGGTGTCGCCCAGCAATACCCGCGTTTGCGCATCGACCAGCGTGCCGG  >  NC_002947/5608431‑5608714

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.