New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	974820 =	56 (1.110)	4 (0.090)	4/234	NT	8.4%	coding (212/543 nt)	ycfJ	flagella biosyntheis regulator
	?	NC_002947	974890 =	36 (0.790)					coding (282/543 nt)	ycfJ	flagella biosyntheis regulator

GTGAAAACCCCGCGTGAAGTTTGCAAGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCAAACCCGCTGCAACACGGTCAACGACATCAGTGAGAAGGTGGTGGGCTACAAC  >  NC_002947/974747‑975037                                                                                                                                                |                                                                                                                                                    gTGAAAACCCCGCGTGAAGTTTGCAAGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGAt                                                                                                                                                >  8:68341/1‑149 (MQ=255)    aaaaCCCCGCGTGAAGTTTGCAAGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGc                                                                                                                                             >  3:113583/1‑149 (MQ=255)        ccccGCGTGAAGTTTGCAAGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGc                                                                                                                                             >  6:118524/1‑145 (MQ=255)        ccccGCGTGAAGTTTGCAAGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGc                                                                                                                                             <  5:118524/145‑1 (MQ=255)          ccGCGTGAAGTTTGCAAGGACGGGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACAACAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGt                                                                                                                                       <  2:153008/149‑1 (MQ=255)           cgcgTGAAGTTTGCAAGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTg                                                                                                                                      >  4:83577/1‑149 (MQ=255)                  aggttGCATGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTg                                                                                                                               <  4:192854/146‑1 (MQ=255)                  aGTTTGCAAGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTg                                                                                                                               <  3:83577/149‑1 (MQ=255)                   gTTTGCAAGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGc                                                                                                                              >  5:191254/1‑149 (MQ=255)                         aaGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCCGTACCGGCAACAAGATTGCCAAGGTTGCAGGTCcagtcgg                                                                                                                        >  8:77372/1‑149 (MQ=255)                          aGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGcggtcggt                                                                                                                       <  6:91988/149‑1 (MQ=255)                             aCGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCggtggt                                                                                                                    <  3:160098/149‑1 (MQ=255)                             aCGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCggtggt                                                                                                                    <  3:196640/149‑1 (MQ=255)                             aCGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCggtggt                                                                                                                    <  7:68341/149‑1 (MQ=255)                                   cTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTAt                                                                                                              <  2:206574/149‑1 (MQ=255)                                       gACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCgg                                                                                                          >  4:163433/1‑149 (MQ=255)                                              cAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAAc                                                                                                     >  8:238313/1‑147 (MQ=255)                                                    ccGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGcggtc                                                                                                                          <  2:38878/120‑1 (MQ=255)                                                    ccGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGcggtc                                                                                                                          >  1:38878/1‑120 (MQ=255)                                                    ccGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCAGTCGGTGGTGGTTATGCGGGTAACAAGGTGCa                                                                                             <  7:77372/149‑1 (MQ=255)                                                       gacAAGGATCAACACCAGATTGCCGGTACCGTCGTCGGTGCGTTGGCAGGTGGTCAGTTGGGTAACCAGATTGGTGGAGGTACCCGCAAGAAGATTGACAACGTGGCCGCTCCGGTCGGTGGTGGGTATGCGGGTATCAAGGTGCAgg                                                                                           >  4:100875/3‑148 (MQ=255)                                                       gTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAgg                                                                                           >  6:174378/1‑148 (MQ=255)                                                                  acacCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAgg                                                                               <  7:238313/149‑1 (MQ=255)                                                                   cacCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCCGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGCAAGGCATGCAg                                                                                >  7:141366/1‑147 (MQ=255)                                                                      cAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCg                                                                           >  5:130293/1‑149 (MQ=255)                                                                          ttgccggtaccgccaccaatctggttacccaacagaccacctgccaacgcaccgaccacggtaccggcaaGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTa                                                                                                       <  1:230183‑M2/47‑1 (MQ=255)                                                                          ttgccggtaccgccaccaatctggttacccaacagaccacctgccaacgcaccgaccacggtaccggcaaGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTa                                                                                                       >  2:230183‑M2/71‑117 (MQ=255)                                                                             ccggtaccgccaccaatctggttacccaacagaccacctgccaacgcaccgaccacggtaccggcaaGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCg                                                                           >  5:226359‑M2/68‑142 (MQ=255)                                                                             ccggtaccgccaccaatctggttacccaacagaccacctgccaacgcaccgaccacggtaccggcaaGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCg                                                                           <  6:226359‑M2/75‑1 (MQ=255)                                                                             CCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATAc                                                                     >  4:113583‑M1/1‑148 (MQ=255)                                                                                GTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTa                                                                  <  5:266744‑M1/148‑1 (MQ=255)                                                                                           ggTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGc                                                       <  6:266744/148‑1 (MQ=255)                                                                                            gTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCg                                                                           >  1:112312/1‑127 (MQ=255)                                                                                            gTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCg                                                                           <  2:112312/127‑1 (MQ=255)                                                                                                     cAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCAAACCCGCTg                                             >  8:12844/1‑148 (MQ=255)                                                                                                         tggtCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGt                                                                                                                                >  1:98156/1‑61 (MQ=255)                                                                                                         tggtCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGt                                                                                                                                <  2:98156/61‑1 (MQ=255)                                                                                                                ttGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCAAACCCGCTGCAACACGGTCaa                                 <  6:191254/149‑1 (MQ=255)                                                                                                                   ggTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCAAACCCGCTGCAACACGGTCAACGa                              >  2:246512/1‑149 (MQ=255)                                                                                                                           gATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCAAACCCGCTGCAACACGGTCAACGACATCAGTg                      <  6:130293/149‑1 (MQ=255)                                                                                                                            aTTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCaaa                                                    >  4:163903/1‑118 (MQ=255)                                                                                                                            aTTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCaaa                                                    <  3:163903/118‑1 (MQ=255)                                                                                                                                   gCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCAAACCCGCTGCAACACGGTCAACGACATCAGTGAGAAggtg              <  5:174378/149‑1 (MQ=255)                                                                                                                                           ggcaaGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCAAACCCGCTGCAACACGGTCAACGACATCAGTGAGAAGGTGGTGGGCTa      >  2:94942‑M2/6‑149 (MQ=255)                                                                                                                                               tgaagaTTGCCTCGGTGGGCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCAAACCCGCTGCAACACGGTGAACGACATCAGTGAGAAGGTTGTGGGCTACAAc  <  8:141366/148‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                    GTGAAAACCCCGCGTGAAGTTTGCAAGGACGTGACTGTGACGCGCCAGGCGCCGGTCAAGGATCAACACCAGATTGCCGGTACCGTGGTCGGTGCGTTGGCAGGTGGTCTGTTGGGTAACCAGATTGGTGGCGGTACCGGCAAGAAGATTGCCACGGTGGCCGGTGCGGTCGGTGGTGGTTATGCGGGTAACAAGGTGCAGGAAGGCATGCAGGAGCGTGATACCTACACAACCACGCAAACCCGCTGCAACACGGTCAACGACATCAGTGAGAAGGTGGTGGGCTACAAC  >  NC_002947/974747‑975037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ 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.