New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 2472140	21 (0.320)	7 (0.150)	5/186	NT	25.1%	intergenic (+44/+105)	PP_2166/PP_2167	anti‑anti‑sigma factor/PhoD‑like phosphatase
	?	NC_002947	= 2472186	27 (0.590)					intergenic (+90/+59)	PP_2166/PP_2167	anti‑anti‑sigma factor/PhoD‑like phosphatase

AATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTGTTCATCA  >  NC_002947/2472040‑2472326                                                                                                                                                   |                                                                                                                                             aaTGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTg                                                                                                                                             >  1:100569‑M2/1‑147 (MQ=255) aaTGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTg                                                                                                                                             >  6:219070‑M2/1‑147 (MQ=255) aaTGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTg                                                                                                                                             <  5:219070‑M2/148‑2 (MQ=255)  aTGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgta                                                                                                                                           >  8:109296‑M2/1‑146 (MQ=255)  aTGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgta                                                                                                                                           >  4:72617‑M2/1‑146 (MQ=255)         cAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagc                                                                                                                                      >  5:312621‑M2/1‑139 (MQ=255)          aaCCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcggg                                                                                                                                   >  3:197688‑M2/1‑138 (MQ=255)          aaCCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgg                                                                                                                                    >  1:144280‑M2/1‑138 (MQ=255)               cgAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgt                                                                                                                                            <  2:351090‑M2/135‑3 (MQ=255)               cgAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgt                                                                                                                                            >  1:351090‑M2/1‑133 (MQ=255)                        ccATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttacccgcgaag                                                                                                                      >  5:4702‑M2/1‑124 (MQ=255)                                                                   tgtgCCGGCCTCTTCTCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttaccc                                                                                                                            >  4:320018‑M2/1‑81 (MQ=255)                                                                   tgtgCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttaccc                                                                                                                            <  3:320018‑M2/99‑19 (MQ=255)                                                                                       tAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTc                                                      >  2:370265/1‑149 (MQ=255)                                                                                            ccGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttacccgcgaagaggccggcacaggctatagatcagctccgctccagcgcattgaccagatcatggaaggcttcgcggttg                                                 <  2:174397‑M2/149‑94 (MQ=255)                                                                                            ccGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttacccgcgaagaggccggcacaggctatagatcagctccgctccagcgcattgaccagatcatggaaggcttcgcggttg                                                 <  3:122338‑M2/149‑94 (MQ=255)                                                                                            ccGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttacccgcgaagaggccggcacaggctatagatcagctccgctccagcgcattgaccagatcatggaaggcttcgcggttg                                                 <  4:185270‑M2/149‑94 (MQ=255)                                                                                            ccGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTa                                                           <  4:248111/139‑1 (MQ=255)                                                                                            ccGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTa                                                           >  3:248111/1‑139 (MQ=255)                                                                                            ccGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCAcccc                                                 >  2:13742/1‑149 (MQ=255)                                                                                             cGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttacccgcgaagaggccggcacaggctatagatcagctccgctccagcgcattgaccagatcatggaaggcttcgcggttg                                                 <  7:96580‑M2/148‑94 (MQ=255)                                                                                              gCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttacccgcgaagaggccggcacaggctatagatcagctccgctccagcgcattgaccagatcatggaaggcttcgcggttgga                                               >  4:122338‑M2/1‑54 (MQ=255)                                                                                                  cTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttacccgcgaagaggccggcacaggctatagatcagctccgctccagcgcattgaccagatcatggaaggcttcgcggttggagtca                                           <  7:298881‑M2/149‑100 (MQ=255)                                                                                                  cTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTgtaggagcgggtttacccgcgaagaggccggcacaggctatagatcagctccgctccagcgcattgaccagatcatggaaggcttcgcggttggagtca                                           >  8:298881‑M2/1‑50 (MQ=255)                                                                                                   tACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTaaa                                                                  >  3:354347/1‑125 (MQ=255)                                                                                                   tACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTaaa                                                                  <  4:354347/125‑1 (MQ=255)                                                                                                    acgacgGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCCCTACGCCGGGTGTTTAAACTCTGTAGCCTCACCCCCGCCAGCa                                         >  7:53885/1‑149 (MQ=255)                                                                                                      gacgGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCAGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATc                                       >  2:118503/1‑149 (MQ=255)                                                                                                               cgcCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTa                              <  1:118503/149‑1 (MQ=255)                                                                                                                 cccAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGAAAAAACTCTGAAACTCACTCCGCCCGGTTATTAAACTCTCTAGCCTCCCCCACGCAAGCATCCCGCTGGGacc                            >  8:140835/1‑148 (MQ=25)                                                                                                                  ccAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTacac                           >  4:217921/1‑149 (MQ=255)                                                                                                                   cAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATc                                       >  4:167661/1‑136 (MQ=255)                                                                                                                   cAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATc                                       <  3:167661/136‑1 (MQ=255)                                                                                                                    aaaCACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACAccc                         >  3:285451/1‑149 (MQ=255)                                                                                                                      acacCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCcgc                       <  3:217921/149‑1 (MQ=255)                                                                                                                        acCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCa                                                                                    <  1:87261/86‑1 (MQ=255)                                                                                                                        acCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCa                                                                                    >  2:87261/1‑86 (MQ=255)                                                                                                                          cAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTac                             <  4:292104/139‑1 (MQ=255)                                                                                                                          cAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTac                             >  3:292104/1‑139 (MQ=255)                                                                                                                              gtgtgtCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCgccggccg               >  3:362399/1‑149 (MQ=255)                                                                                                                                  gtCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGcccc           >  4:83457/1‑149 (MQ=255)                                                                                                                                   tCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCt          >  6:246206/1‑149 (MQ=255)                                                                                                                                     cACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTg         <  1:370265/148‑1 (MQ=255)                                                                                                                                     cACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTg         <  3:83457/148‑1 (MQ=255)                                                                                                                                     cACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTGt        >  2:7378/1‑149 (MQ=255)                                                                                                                                       cccccAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTGtt       >  4:80777/1‑148 (MQ=255)                                                                                                                                            aaTCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTGTtcatca  >  6:190017/1‑148 (MQ=255)                                                                                                                                                   |                                                                                                                                             AATGACTCCAACCGCGAAGCCTTCCATGATCTGGTCAATGCGCTGGAGCGGAGCTGATCTATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGACGGCCTGCGCCCAAACACCAATGTGTGTCCACCCCCAATCAGGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCTGTAAAAACTCTGAATCTCACTACGCCCGGTTTTTAAACTCTGTAGCCTCACCCCCGCCAGCATCCAGCTGGTACACCCGCGCCGGCCGCCCCTGTTCATCA  >  NC_002947/2472040‑2472326

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.