New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	4114305 =	38 (0.580)	3 (0.050)	3/238	NT	8.9%	intergenic (+52/+94)	PP_3619/ycaO	hypothetical protein/ribosomal protein S12 methylthiotransferase accessory factor
	?	NC_002947	4114376 =	27 (0.460)					intergenic (+123/+23)	PP_3619/ycaO	hypothetical protein/ribosomal protein S12 methylthiotransferase accessory factor

CTCTCTGTTGGTACTGTGTCTGCAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTGCAGCTTCTTGTAGCTGTCGATCAGG  >  NC_002947/4114159‑4114450                                                                                                                                                   |                                                                                                                                                     ctctctGTTGGTACTGTGTCTGCAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCgg                                                                                                                                                    >  4:88357/1‑149 (MQ=255)    ggcagtgtccgcttccatggcctgaccccgaccagcatgaagctcgaaggccttgatcgccacctgcgcctgatcgacagctacaagaagctgcacgcggcccgggccaagttcgcctgacaggcgctgcgcccaatcatcgcCGGc                                                                                                                                                   <  5:173426‑M1/4‑1 (MQ=255)      tGTTGGTACTGTGTCTGCAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTTAAGTGGATAGGAAGAGAACGCTATGCGCCTTGATGGCAACGCGGCaa                                                                                                                                                 <  1:92996/147‑1 (MQ=255)       agtgtccgcttccatggcctgaccccgaccagcatgaagctcgaaggccttgatcgccacctgcgcctgatcgacagctacaagaagctgcacgcggcccgggccaagttcgcctgacaggcgctgcgcccaatcatcgcCGGCAAGcc                                                                                                                                              <  4:243480‑M1/9‑1 (MQ=255)       agtgtccgcttccatggcctgaccccgaccagcatgaagctcgaaggccttgatcgccacctgcgcctgatcgacagctacaagaagctgcacgcggcccgggccaagttcgcctgacaggcgctgcgcccaatcatcgcCGGCAAGcc                                                                                                                                              <  3:46779‑M1/9‑1 (MQ=255)        ttGGTACTGTGTCTGCAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCa                                                                                                                                             <  8:314997/149‑1 (MQ=255)          gtccgcttccatggcctgaccccgaccagcatgaagctcgaaggccttgatcgccacctgcgcctgatcgacagctacaagaagctgcacgcggcccgggccaagttcgcctgacaggcgctgcgcccaatcatcgcCGGCAAGCCAGc                                                                                                                                           <  8:30799‑M1/12‑1 (MQ=255)           tccgcttccatggcctgaccccgaccagcatgaagctcgaaggccttgatcgccacctgcgcctgatcgacagctacaagaagctgcacgcggcccgggccaagttcgcctgacaggcgctgcgcccaatcatcgcCGGCAAGCCAGc                                                                                                                                           >  3:170690‑M1/137‑148 (MQ=255)             aCTGTGTCTGCAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTc                                                                                                                                        >  1:355237/1‑149 (MQ=255)              cTGTGTCTGCAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTc                                                                                                                                        <  3:192921/148‑1 (MQ=255)                gtgtCTGCAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCAAGCGTAca                                                                                                                                      >  3:113836/1‑148 (MQ=255)                     tGCAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGtt                                                                                                                                >  2:286562/1‑149 (MQ=255)                       cAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTc                                                                                                                               <  6:113149/148‑1 (MQ=255)                       cAAGCTTTACAATGTCCGTGCAGCGCCACCACCGGCGGAGGCATTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACATGTTcc                                                                                                                              >  5:289104/1‑148 (MQ=255)                        aaGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑gg                                                                                                                           >  1:323335/1‑149 (MQ=255)                        aaGCTTTTCAATGACCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCCCCTGAAGTGGATAGGCAGAGACCGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑gg                                                                                                                           <  4:347395/149‑1 (MQ=255)                            ttttCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGca                                                                                                                         >  8:91192/1‑147 (MQ=255)                                cAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCAGGATGGCAACGCGGCAAGCCAGCGTCCACACGTTC‑‑GGCACAGAt                                                                                                                    >  4:68462/1‑148 (MQ=255)                                 aaTGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCTAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑TGCACAGAtct                                                                                                                  <  3:68462/149‑1 (MQ=255)                                  aTGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGAtct                                                                                                                  >  6:391754/1‑148 (MQ=255)                                    gTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGAtctc                                                                                                                 >  7:194718/1‑147 (MQ=255)                                    gTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGAtctc                                                                                                                 >  7:55215/1‑147 (MQ=255)                                     tCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAag                                                                                                              <  3:80306/149‑1 (MQ=255)                                           cAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGTAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGt                                                                                                        <  8:194718/149‑1 (MQ=255)                                             gcgcCACCACCGGGGGAGGCTTTAGAAAGTGGGCCTGCTAAGCCCGAATAGTCAGCACCTGTAGTGGATAGGAAGAGTACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGc                                                                                                      <  5:332551/149‑1 (MQ=255)                                                 caccacCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACCGCTCTTGAGATCTGTGccgaa                                                                                                  <  6:120886/149‑5 (MQ=38)                                                    caccGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCt                                                                                               <  4:314214/149‑1 (MQ=255)                                                           atcgccacctgcgcctgatcgacagctacaagaagctgcacgcggcccgggccaagttcgcctgacaggcgctgcgcccaatcatcgcCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGgcg‑c                                                                                       >  2:87734‑M1/89‑149 (MQ=255)                                                            gAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCG‑CCACAGGTAT‑‑TGCACCGCTCTTGAGATCTGTGCCGAACCTGTggacgct                                                                                      <  7:15531/149‑6 (MQ=18)                                                             aGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTg                                                                                     <  2:323335/149‑1 (MQ=255)                                                              ggCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTgg                                                                                    <  3:88357/149‑1 (MQ=255)                                                                cTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCt                                                                                  >  2:89470/1‑149 (MQ=255)                                                                   tCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCtt                                                                                 <  2:355237/147‑1 (MQ=255)                                                                                  cTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACACGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGgc                                                                >  7:326038/1‑149 (MQ=255)                                                                                                  accaccTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGc                                                <  7:91192/149‑1 (MQ=255)                                                                                                  accaccTGAAGTGGAAAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTCGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGc                                                >  8:304560/1‑149 (MQ=255)                                                                                                          aaGTGTATAGCAACAGAACGCTAGGCGCCTGGAGGGCAACGCGGCAAGCCAGCGCCCACAGGTGC‑‑GGCACACATCTCAAGCGCGGTGCAATACCTGTGGCG‑CCGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTg                                         <  1:286562/148‑1 (MQ=255)                                                                                                          aaGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGGGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTgg                                        <  5:391754/149‑1 (MQ=255)                                                                                                          aaGTGGATAGGAAGACAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAACAGCGGTGCAATACCTGTGGCGCCTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACtt                                          <  1:89470/148‑1 (MQ=255)                                                                                                                aTAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTCGAGGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCg                                    >  1:320446/1‑149 (MQ=255)                                                                                                                       gagaACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTg                           >  6:74122/1‑149 (MQ=255)                                                                                                                              cTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGAGTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTGCAGcttc                    >  3:47164/1‑149 (MQ=255)                                                                                                                                 tGCACCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTGCAGCTTCTTg                 <  5:307739/149‑1 (MQ=255)                                                                                                                                   tgcgcccaatcatcgcCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATAc                                                                                                 <  3:323318‑M1/52‑1 (MQ=255)                                                                                                                                   tgcgcccaatcatcgcCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATAc                                                                                                 >  4:323318‑M1/17‑68 (MQ=255)                                                                                                                                      cTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTGCAGcttct                   >  3:8347/1‑142 (MQ=255)                                                                                                                                           tGGCAAGGCGCCATGCCAGCGTCCACAGGTTG‑‑GGCACATATCTCATGAGCGGTGCAATACGTGTGGCG‑GTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTGCAGCTTCTTGTAGCTGTCg        <  2:320446/148‑1 (MQ=255)                                                                                                                                              cAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTGCAGCTTCTTGTAGCTGTCGAt      >  6:173426/1‑147 (MQ=255)                                                                                                                                               aaCGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTGCAGCTTCTTGTAGCTGTCGATCAg   >  1:183995/1‑149 (MQ=255)                                                                                                                                                aCGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTGCAGCTTCTTGTAGCTGTCGATCAgg  >  3:243480/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                     CTCTCTGTTGGTACTGTGTCTGCAAGCTTTTCAATGTCCGTGCAGCGCCACCACCGGCGGAGGCTTTCGAAAGTGGGCCTGCTAAGCCCGAATAGTCACCACCTGAAGTGGATAGGAAGAGAACGCTATGCGCCTGGATGGCAACGCGGCAAGCCAGCGTCCACAGGTTC‑‑GGCACAGATCTCAAGAGCGGTGCAATACCTGTGGCG‑CTGGCTTGCCGGCGATGATTGGGCGCAGCGCCTGTCAGGCGAACTTGGCCCGGGCCGCGTGCAGCTTCTTGTAGCTGTCGATCAGG  >  NC_002947/4114159‑4114450

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ 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.