New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 3947984	35 (0.580)	3 (0.070)	3/184	NT	7.6%	coding (109/1797 nt)	PP_3483	type II secretion system protein
	?	NC_002947	= 3948013	46 (1.000)					coding (80/1797 nt)	PP_3483	type II secretion system protein

AGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/3947815‑3947984 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tcttcgcgggcatgcccgctcccacaggATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTGCTCGACTGCCTGG  <  NC_002947/3948013‑3947870                                                                                                                                                                                                                                                                                                                            AGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGag                                                                                                                                                                      >  1:1572825/1‑148  GGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGG                                                                                                                                                                     <  1:1053939/150‑1     TCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCA                                                                                                                                                                  <  1:944952/150‑1     TCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCA                                                                                                                                                                  >  1:1444612/1‑150      CAGGCCCAGGCGCCGGGTAAAGGGGTCGGGGGTGTCGCAGGCCAAGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGAGCAAGAGGCCGCGGGGGTAGTTGAAAATTTTTTCTGCGTTCTTCGCAGGCAT                                                                                                                                                                 <  2:1334047/150‑1        GGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGC                                                                                                                                                               <  2:1590842/150‑1          CCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCC                                                                                                                                                             >  2:848960/1‑150            CAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGC                                                                                                                                                           >  1:917204/1‑150                   CGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACA                                                                                                                                                    <  2:1459746/150‑1                   CGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACA                                                                                                                                                    <  2:172922/150‑1                    GGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAG                                                                                                                                                   <  2:1054210/150‑1                     GGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAGG                                                                                                                                                  >  2:335120/1‑150                                     GTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACA                                                                                                                                                    >  2:738814/1‑132                                     GTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACA                                                                                                                                                    <  1:738814/132‑1                                                CAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTC                                                                                                                                                                         <  2:1494967/100‑1                                                CAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTC                                                                                                                                                                         >  1:1494967/1‑100                                                 AGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAG                                                                                                                                                   <  2:1441352/121‑1                                                 AGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAG                                                                                                                                                   >  1:1441352/1‑121                                                           GGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGG                                                                                                                                                                     <  1:1361864/93‑1                                                           GGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGG                                                                                                                                                                     >  2:1361864/1‑93                                                              AGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCG                                                                                                         <  1:581182/150‑1                                                                              GTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAG                                                                                                                                                   <  1:613144/92‑1                                                                              GTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAG                                                                                                                                                   >  2:613144/1‑92                                                                                                                    GGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATG                                                                                                                                                                >  2:1588010/1‑41                                                                                                                    GGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATG                                                                                                                                                                <  1:1588010/41‑1                                                                                                                        GTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGC                                                                                                  <  1:1040172/99‑1                                                                                                                        GTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGC                                                                                                  >  2:1040172/1‑99                                                                                                                            GCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACA                                                                                                                                                    >  2:980451/1‑45                                                                                                                            GCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACA                                                                                                                                                    <  1:980451/45‑1                                                                                                                                               TCTTCGCGGGCATGCCCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTG                                                                                                               >  1:335697/1‑63                                                                                                                                               TCTTCGCGGGCATGCCCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTG                                                                                                               <  2:335697/63‑1                                                                                                                                                 TTCGCGGGCATGCCCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGCGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCCCGGCCTCCTGGCGCAGCCCCGTCTGCAAGCCACTGACGA                      >  2:956427/1‑150                                                                                                                                                      GGGCATGCCCGCTCCCACAGGATGTATGGAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCC                                                              >  1:809492/1‑105                                                                                                                                                      GGGCATGCCCGCTCCCACAGGATGTATGGAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCC                                                              <  2:809492/105‑1                                                                                                                                                        GCATGCCCGCTCCCACAGGATGTATGCAGCCGACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTG               >  2:1011233/1‑150                                                                                                                                                          ATGCCCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCG                                                                       >  1:330464/1‑92                                                                                                                                                          ATGCCCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCG                                                                       <  2:330464/92‑1                                                                                                                                                           gGCCCGCTCCGACAGGATGTATGCAGCCCACAGACCTTTGATGTACTCGTGGTGGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTGCTC            <  2:543823/149‑1                                                                                                                                                              CCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTGCTCGAC         >  1:799602/1‑150                                                                                                                                                              CCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTGCTCGAC         >  1:799490/1‑150                                                                                                                                                              CCGCTCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCCACCTCCTGGCCCAGGCCCGTCTGCAAGCAACTGACGAGCGCCTGCTCGcc         >  2:595146/1‑148                                                                                                                                                               gatctCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAACTTTCCGCCTACCCCCGCGTCCTCCTTAGCCAGTCCCGTCTGCAAGCCACTGACGAGCGCCTGCTCGACT        <  1:1519195/145‑1                                                                                                                                                                  TCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGAC                                                         <  2:1350465/98‑1                                                                                                                                                                  TCCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGAC                                                         >  1:1350465/1‑98                                                                                                                                                                   CCCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTGCTCGACTGCCT    <  1:1011233/150‑1                                                                                                                                                                    CCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTGCTCGACTGCCTG   >  1:1584721/1‑150                                                                                                                                                                    CCACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATCTAGGTATACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTGCTCGACTGCCTG   >  1:848960/1‑150                                                                                                                                                                     CACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTGCTCGACTGagatc  >  2:1519195/1‑145                                                                                                                                                                      ACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTC                                                      >  1:1607424/1‑97                                                                                                                                                                      ACAGGATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTC                                                      <  2:1607424/97‑1                                                                                                                                                                                                                                                                                                                            AGGGTCAGGCCCAGGCGCCGGGTGAAGGTGTCGGGGGTGTCGCAGGCCAGGCGTTCCAGGCAGTCGAGCAGGCGCTCGTCAGTGGCTTGCAGACGGGCCTGGGCCAGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/3947815‑3947984 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tcttcgcgggcatgcccgctcccacaggATGTATGCAGCCCACAGACCTGTGATGTACCTGTGGGAGCGGGCATGCCCGCGAAGAACCCAGCAAAAATTTCCGCCTACCCCCGCGACCTCCTGGCCCAGGCCCGTCTGCAAGCCACTGACGAGCGCCTGCTCGACTGCCTGG  <  NC_002947/3948013‑3947870

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.