New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 3511747	43 (0.880)	3 (0.060)	4/238	NT	6.5%	coding (372/4158 nt)	PP_3108	rhs family protein
	?	NC_002947	= 3511759	45 (0.960)					coding (384/4158 nt)	PP_3108	rhs family protein

CACTGCCTCACCCAACGTGTTCATCAACAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTGCGCACCACCGTGGATGTGCTGATGGCCATCGCCG  >  NC_002947/3511612‑3511904                                                                                                                                                     |                                                                                                                                                   cACTGCCTCACCCAACGTGTTCATCAACAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGgg                                                                                                                                                  >  2:984228‑M2/1‑148 (MQ=255) cACTGCCTCACCCAACGTGTTCATCAACAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGgg                                                                                                                                                  <  2:1182746‑M2/150‑3 (MQ=255)  aCTGCCTCACCCAACGTGTTCATCAACAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGggc                                                                                                                                                 >  2:1198929‑M2/1‑147 (MQ=255)           cccAACGTGTTCATCAACAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTg                                                                                                                                        <  2:486032/150‑1 (MQ=255)                        tcaACAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGcca                                                                                                                           >  1:1077112/1‑150 (MQ=255)                        tcaACAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGcca                                                                                                                           >  1:831937/1‑150 (MQ=255)                          aaCAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGccacc                                                                                                                         >  1:624151/1‑150 (MQ=255)                           aCAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGccacca                                                                                                                        >  2:1272995/1‑150 (MQ=255)                                cGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGAc                                                                                                                                      <  2:742904/131‑1 (MQ=255)                                cGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGAc                                                                                                                                      >  1:742904/1‑131 (MQ=255)                                 gCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCg                                                                                                                 <  2:380025/150‑1 (MQ=255)                                        cgcccgcGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTc                                                                                                          <  2:837366/150‑1 (MQ=255)                                           ccgcGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGG‑GCCGATTGCCGCAAGCCCGACCAACGTCCTCAACAAAAAGCGCCG‑CGCCCCGCCGAAAGGGGACAAGCCGCCCTTCCGCCCCACCAAT‑TCCCGTGGGTCCGAc                                                                                                      >  2:769574/1‑150 (MQ=255)                                               gTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAAc                                                                                                   >  2:193102/1‑150 (MQ=255)                                                   aaaaaaGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGtca                                                                                               >  2:189007/1‑150 (MQ=255)                                                          cATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATcgg                                                                                        <  1:1182746/150‑1 (MQ=255)                                                              ggTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTAGGACAACGTCATCATcggcggc                                                                                    <  1:693576/150‑1 (MQ=255)                                                                  ccTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCa                                                                                <  1:142104/150‑1 (MQ=255)                                                                   cTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCCTTGCGCGCGGCggcgacgctgt                                                                                                                                         >  1:28095‑M2/1‑82 (MQ=255)                                                                                ccAGGGCCGGTGCAGATTGCCG‑AGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCatcatc                                                                                          <  1:1236049/125‑1 (MQ=255)                                                                                ccAGGGCCGGTGCAGATTGCCG‑AGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCatcatc                                                                                          >  2:1236049/1‑125 (MQ=255)                                                                                           gCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCTGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGa                                                       <  1:620944/150‑1 (MQ=255)                                                                                              gATTGGCGCAGGCTCGATCAACGTCTTCATC‑AACAGCGTCGCCGCCTCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGGTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGa                                                    <  2:593141/150‑1 (MQ=255)                                                                                               cgatctgAAGGCTCGACCCACGTCTTCATC‑AACACCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTCCGATG‑TTCCATTCTCCACCGACACGGGCATGGACAAGATCATCGCCGCGACCTACCGTTACCTGCCCGTGGACGATGaa                                                   <  1:23551/144‑1 (MQ=255)                                                                                               aTTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGaa                                                   <  2:32023/150‑1 (MQ=255)                                                                                                   ccGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGggcgacgctgttgatgaagacgttgg                                                                                                                          >  2:445321‑M2/1‑50 (MQ=255)                                                                                                   ccGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGggcgacgctgttgatgaagacgttgg                                                                                                                          <  1:445321‑M2/76‑27 (MQ=255)                                                                                                    cGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTccc                                              >  2:154498/1‑150 (MQ=255)                                                                                                     gAAGGCTCGACCAACGTCTTCATC‑AACATCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCg                                             >  1:376296/1‑150 (MQ=255)                                                                                                      aaGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAgagatcg                                            >  2:23551/1‑144 (MQ=255)                                                                                                       aGGCTCGACCACCGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGa                                           <  1:328645/150‑1 (MQ=255)                                                                                                          cTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATg                                                     <  2:1207429/137‑1 (MQ=255)                                                                                                          cTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATg                                                     >  1:1207429/1‑137 (MQ=255)                                                                                                           tCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTgg                                       >  1:951829/1‑150 (MQ=255)                                                                                                           tCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTgg                                       <  2:624151/150‑1 (MQ=255)                                                                                                             gACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGa                                                          <  1:1106813/129‑1 (MQ=255)                                                                                                             gACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGa                                                          >  2:1106813/1‑129 (MQ=255)                                                                                                             gACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCt                                     >  1:662126/1‑150 (MQ=255)                                                                                                               ccAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTgc                                   >  1:1052459/1‑150 (MQ=255)                                                                                                                cAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGtc                                                                                                <  2:1066825/88‑1 (MQ=255)                                                                                                                cAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTgcg                                  >  1:75880/1‑150 (MQ=255)                                                                                                                cAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGAAAGTGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGtc                                                                                                >  1:1066825/1‑88 (MQ=255)                                                                                                                         catc‑aACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTa                                                                            <  1:925897/99‑1 (MQ=255)                                                                                                                         catc‑aACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTa                                                                            >  2:925897/1‑99 (MQ=255)                                                                                                                         catc‑aACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTGCGCACCACCGt                         >  1:406340/1‑150 (MQ=255)                                                                                                                               aCAGCGTCGCCGCCGCGCGCAAGggcgacgctgttgatgaagacgttggtcgagccttcggcaatctgcaccggccctgggtgcttgtcgcag                                                                              >  2:28095‑M2/1‑23 (MQ=255)                                                                                                                               aCAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGTTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTGCGCACCACCGTGGAtg                    >  2:888717/1‑150 (MQ=255)                                                                                                                                    gTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCTGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTGCGCACCACCGTGGATGTGCTg               >  2:700874/1‑150 (MQ=255)                                                                                                                                       gccgccgcGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGtca                                                                                               <  2:358605/67‑1 (MQ=255)                                                                                                                                       gccgccgcGCGCAAGGGCGACAAGCTGACATGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGtca                                                                                               >  1:358605/1‑67 (MQ=255)                                                                                                                                        ccgccgcGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTGCGCACCACCGTGGATGTGCTGATgg           <  1:986241/150‑1 (MQ=255)                                                                                                                                             gcgcgcAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTGCGCACCACCGTGGATGTGCTGATGGCCATc      >  2:52580/1‑150 (MQ=255)                                                                                                                                                 gcAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGTTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTGCGCACCACCGTGGATGTGCTGATGGCCATCGCCg  <  1:888717/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                   CACTGCCTCACCCAACGTGTTCATCAACAGCCGCAAGGCCGCCCGCGTCGAAAAAAGCATCGGTGCCTGCGACAAGCACCCAGGGCCGGTGCAGATTGCCGAAGGCTCGACCAACGTCTTCATC‑AACAGCGTCGCCGCCGCGCGCAAGGGCGACAAGCTGACCTGCGGCGCCACCATT‑TCCGGTGGTTCGGACAACGTCATCATCGGCGGCGGCACCTACCGTTACCTGCCCGTGGACGATGAAGTCCCGGAGTGGCTGCGCACCACCGTGGATGTGCTGATGGCCATCGCCG  >  NC_002947/3511612‑3511904

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.