New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	1196535 =	32 (0.780)	4 (0.100)	3/320	NT	10.5%	coding (596/1755 nt)	xcpQ	Type II secretion pathway protein XcpQ
	?	AE015451	1196595 =	38 (0.980)					coding (656/1755 nt)	xcpQ	Type II secretion pathway protein XcpQ

CAGCAGGGCGAGGGCAGCGACAGCGTGGCCACCCGCGTATTCAGCGTGCGCAACGCCGCCAGCGAACAGGTACTGGGCATCCTCAAACCGCTGATCGACCCGCGAGTTGGGGTTATTACACCGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGAATACGAAGAAGGTACCAATGCCGTGGTCATGGTCGGCCCCGACAGCGAGCTGGCGGCGTACCGGG  >  AE015451/1196306‑1196765                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                       ggcgatgatcgcttcgaccaccacctgggcacggcgaatatccagttgctcgacaatggcccggtacgccgccagctcgctgtcggggccgaccatgaccacggcattggtaccttcttcgtattccaggcggatgcccgagccaccggcggctggcaccaccggccggtccttgccctctgcctcacccgcgccttcaaccggcaccgccccttcgtggctgagccctcgcagca                                                                                                                                                                                                                                   <  1:392323‑M1/6‑1 (MQ=255)                                      tATTCAGCGTGCGCAACGCCGCCAGCGAACAGGTACTGGGCATCCTCAAACCGCTGATCGACCCGCGAGTTGGGGTTATTACACCGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAGGCTGGCGATGCGT‑TCGAGGTTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGaa                                                                                                                                                                                             >  1:527463/1‑236 (MQ=255)                                              gTGCGCAACGCCGCCAGCGAACAGGTACTGGGCATCCTCAAACCGCTGATCGACCCGCGAGTTGGGGTTATTACACCGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTg                                                                                                                                                                                                                  <  2:535501/207‑1 (MQ=255)                                                  gcAACGCCGCCAGCGAACAGGTACTGGGCATCCTCAAACCGCTGATCGACCCGCGAGTTGGGGTTATTACACCGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGt                                                                                                                                                                                  >  1:379791/1‑235 (MQ=255)                                                      caatggcccggtacgccgccagctcgctgtcggggccgaccatgaccacggcattggtaccttcttcgtattccaggcggatgcccgagccaccggcggctggcaccaccggccggtccttgccctctgccccacccgcgccttcaaccggcaccgccccttcctggctgagccctcgcc                                                                                                                                                                                                                                      <  2:501005‑M1/3‑2 (MQ=255)                                                                                   tCAAACCGCTGATCGACCCGCGAGTTGGGGTTATTACACCGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGggcagcgacag                                                                                                                                                                                                                                     >  2:187507/1‑151 (MQ=255)                                                                                          gCTGATCGACCCGCGAGTTGGGGTTATTACACCGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTg                                                                                                                                                                                                                  <  2:689240/163‑1 (MQ=255)                                                                                           cTGATCGACCCGCGAGTTGGGGTTATTACCCCGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAgg                                                                                                                                        <  1:125200/236‑1 (MQ=255)                                                                                              aTCGACCCGCGAGTTGGGGTTATTACACCGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCg                                                                                                                                                >  1:738737/1‑225 (MQ=255)                                                                                                                         ccGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGa                                                                                                                                                                           <  2:234918/171‑1 (MQ=255)                                                                                                                             aCCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCa                                                                                                                                                                    >  1:605390/1‑174 (MQ=255)                                                                                                                              cccGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGAccggccg                                                                                                         >  2:716949/1‑232 (MQ=255)                                                                                                                               ccGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCggtggt                                                                                                    >  1:419926/1‑236 (MQ=255)                                                                                                                                 ggcggcGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGgtggtg                                                                                                   >  2:462325/1‑235 (MQ=255)                                                                                                                                      atgcccgagccaccggcggctggcaccaccggccggtccttgccctctgcctcacccgcgccttcaaccggcaccgccccttcctggctgagccctcGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGaa                                                                                                                                          >  1:345058‑M1/98‑192 (MQ=255)                                                                                                                                         aCCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGGGGGCAAGGACCGGCCGGGGGGGCCAgccgcc                                                                                          >  1:174542/1‑236 (MQ=255)                                                                                                                                                      gactgactGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGc                                                                              >  1:496313/1‑235 (MQ=255)                                                                                                                                                        ctgactgGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAgg                                                                                                                             >  1:54677/1‑186 (MQ=255)                                                                                                                                                         tgactgGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTCGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATcc                                                                          <  1:716950/236‑1 (MQ=255)                                                                                                                                                          gacggGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGACAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCACGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCAt                                                                            >  2:392322/1‑233 (MQ=255)                                                                                                                                                              ggCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTg                                                                                                                                                                                          >  1:666461/1‑119 (MQ=255)                                                                                                                                                              ggCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTg                                                                                                                                                                                          <  2:666460/119‑1 (MQ=255)                                                                                                                                                              ggCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGc                                                                        >  2:749483/1‑233 (MQ=255)                                                                                                                                                               gcgcAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTg                                                                     >  1:361022/1‑235 (MQ=255)                                                                                                                                                                cgcAGCACCCTCG‑AACGCATCGCCAGCCTGCTGCGCCCGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGc                                                                              <  1:122854/225‑1 (MQ=255)                                                                                                                                                                   agcaACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGaa                                                                  <  2:361021/234‑1 (MQ=255)                                                                                                                                                                       aCCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGAATACgaa                                                            <  1:462326/236‑1 (MQ=255)                                                                                                                                                                        ccTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGGAGTGGTCAAGGtgctgc                                                                                                                                                                             >  2:95910/1‑122 (MQ=255)                                                                                                                                                                              aaCGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGgtggtg                                                                                                   >  2:756896/1‑191 (MQ=255)                                                                                                                                                                                      gCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGAATACGAAGAAGGTACCaa                                                 >  2:300189/1‑233 (MQ=255)                                                                                                                                                                                       cctcacccgcgccttcaaccggcaccgccccttcctggctgagccctcGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGa                                                                                                                                                                           <  2:342563‑M1/62‑1 (MQ=255)                                                                                                                                                                                       cctcacccgcgccttcaaccggcaccgccccttcctggctgagccctcGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGa                                                                                                                                                                           >  1:342564‑M1/49‑110 (MQ=255)                                                                                                                                                                                       cctcacccgcgccttcaaccggcaccgccccttcctggctgagccctcGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCAGGCGAAGGGGTCAAGGTGCTGCGAGGGCTCAGGCAGGAAGGGGCGGtgcgg                                                                                                                                                <  2:533154‑M1/89‑3 (MQ=255)                                                                                                                                                                                               ctgcGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGaa                                                                                                                                          <  2:586554/135‑1 (MQ=255)                                                                                                                                                                                               cgccgcCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGa                                                                                                                               >  2:671479/4‑146 (MQ=255)                                                                                                                                                                                                     cAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGAATACggagaa                                                         >  1:294701/1‑210 (MQ=255)                                                                                                                                                                                                         tCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGAATACGAAGAAGGTACCAAt                                                <  2:527462/215‑1 (MQ=255)                                                                                                                                                                                                              cGCCCTCACGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAgg                                                                                                                             <  2:241324/133‑1 (MQ=255)                                                                                                                                                                                                                        agGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGAATACGAAGAAGGTACCAATGCCGTGGTCATGGTCGGCCCCGACAGCGAGCTggcg            >  1:33738/1‑236 (MQ=255)                                                                                                                                                                                                                                   agcggcagcACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGAATACGAAGAAGGTACCAATGCCGTGGTCATGGTCGGCCCCGACAGCGAGCTGGCGGCGTACCggg  >  1:741235/1‑235 (MQ=255)                                                                                                                                                                                                                                    gcggcagcACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGAATACGAAGAAGGTACCAATGCCGTGGTCATGGTCGGCCCCGACAGCGAg                  >  1:730646/1‑218 (MQ=255)                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                       CAGCAGGGCGAGGGCAGCGACAGCGTGGCCACCCGCGTATTCAGCGTGCGCAACGCCGCCAGCGAACAGGTACTGGGCATCCTCAAACCGCTGATCGACCCGCGAGTTGGGGTTATTACACCGTACCCGGCGGCGCACCAGTTGGTGGTGACTGACTGGCGCAGCAACCTCG‑AACGCATCGCCAGCCTGCTGCGCCAGCTCGACCGCCCTCAAGAGGTACCGGGCAGCGGCAGCACCCAGGTGATCTACTTGCGCCATGCCAATGCCGGCGAAGTGGTCAAGGTGCTGCGAGGGCTCAGCCAGGAAGGGGCGGTGCCGGTTGAAGGCGCGGGTGAGGCAGAGGGCAAGGACCGGCCGGTGGTGCCAGCCGCCGGTGGCTCGGGCATCCGCCTGGAATACGAAGAAGGTACCAATGCCGTGGTCATGGTCGGCCCCGACAGCGAGCTGGCGGCGTACCGGG  >  AE015451/1196306‑1196765

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ 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.