New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	4980231 =	32 (0.800)	3 (0.080)	3/316	NT	10.7%	intergenic (‑22/+139)	flgF/PP_4387	flagellar basal‑body rod protein FlgF/conserved exported protein of unknown function
	?	AE015451	4980313 =	20 (0.530)					intergenic (‑104/+57)	flgF/PP_4387	flagellar basal‑body rod protein FlgF/conserved exported protein of unknown function

GGCGCTCGGTCATGGCGAATGCACGCGCCGGAAAGCTGTCACCGAACACCGGCATCGAGCGGGCCTGCTCCAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGCTTGCTCAATGGGCGCGGCAGGCGGCGTTGTTGTAGGGGCCAGAGTGGCGCACCCAGCCTTTGCCCGGGTTGTGGGCCGAACACAGGTAGCGGCCGGT  >  AE015451/4980026‑4980462                                                                                                                                                                                                              |                                                                                                                                                                                                                                        ggttctgcctgcccccgctgcccccgccccgttctatcaatggcaaagcctggtcaccggccgctacctgtgttcggcccacaacccgggcaaaggctgggtgcgccactctggcccctacaacaacgccgcctgccgcgcccattgagcaagcccttgccgcaggcggcaaacatccgccgacaaactgacggttattgcccctTGCCGCGCTg                                                                                                                                                                                                                                >  2:257623‑M1/206‑215 (MQ=255)           cATGGCGAATGCACGCGCCGGAAAGCTGTCACCGAACACCGGCATCGAGCGGGCCTGCTCCAAGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTg                                                                                                                                                                                                    <  1:552545/233‑1 (MQ=255)            aTGGCGAATGCACGCGCCGGAAAGCTGTCACCGAACACCGGCATCGAGCGGGCCTGCTCCAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCa                                                                                                                                                                                                               <  1:212517/221‑1 (MQ=255)             tGGCGAATGCACGCGCCGGAAAGCTGTCACCGAACACCGACATCGAGCGGGCCTGCTCCAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTg                                                                                                                                                                                                                          <  2:452673/209‑1 (MQ=255)                                 aaGCTGTCACCGAACACCGGCATCGAGCGGGCCTGCTCCAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAgg                                                                                                                                                                                                                    <  1:586606/195‑1 (MQ=255)                                        cACCGAACACCGGCATCGAGCGGGCCTGCTCCAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACg                                                                                                                                                                         >  2:344839/1‑231 (MQ=255)                                          ccGAACACCGGCATCGAGCGGGCCTGCTCCAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCa                                                                                                                                                                                                               >  2:459945/1‑191 (MQ=255)                                                  cGGCATCGAGCGGGCCTGCTCCAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCgg                                                                                                                                                          <  1:309405/236‑1 (MQ=255)                                                    gCATCGAGCGGGCCTGCTCCAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGa                                                                                                                                                                                                   <  2:280384/193‑1 (MQ=255)                                                                       cAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAAATGaa                                                                                                                                                                                                  >  2:509262/1‑175 (MQ=255)                                                                           tCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCgg                                                                                                                                                          <  2:640325/211‑1 (MQ=255)                                                                                cacaacccgggcaaaggctgggtgcgccactctggcccctacaacaacgccgcctgccgcgcccattgagcaagcccttgccgcaggcggcaaacatccgccgacaaactgacggttattgcccctTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAaca                                                                                                                                                                                    <  1:483717‑M1/54‑1 (MQ=255)                                                                                cacaacccgggcaaaggctgggtgcgccactctggcccctacaacaacgccgcctgccgcgcccattgagcaagcccttgccgcaggcggcaaacatccgccgacaaactgacggttattgcccctTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAaca                                                                                                                                                                                    >  2:483716‑M1/127‑180 (MQ=255)                                                                                           tggtggAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTgcc                                                                                                                  <  1:591219/235‑1 (MQ=255)                                                                                                 aaaTGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCgg                                                                                                                                                          <  2:593808/189‑1 (MQ=255)                                                                                                              gttgttGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCa                                                                                                                                                                                                               <  1:566905/123‑1 (MQ=255)                                                                                                                            ccTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGCTTGCTCAATGGGCGCGGCa                                                                                >  1:321734/1‑236 (MQ=255)                                                                                                                             aacgccgcctgccgcgcccattgagcaagcccttgccgcaggcggcaaacatccgccgacaaactgacggttattgcccctTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTg                                                                                                                                                                                                    >  2:51517‑M1/82‑119 (MQ=255)                                                                                                                                           cggtCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACGTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGa                                                                                                                                                                                                   <  2:2951/103‑1 (MQ=255)                                                                                                                                                tggctggcGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCa                                                                                                                                                                <  2:136402/136‑1 (MQ=255)                                                                                                                                                       cgcCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGCTTGCTCAATGGGCGCGGCAGGCGGCGTTGTTGTAGGGGCCAGAGTg                                                     <  1:344840/236‑1 (MQ=255)                                                                                                                                                          cGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCa                                                                                                                                                                <  1:594673/126‑1 (MQ=255)                                                                                                                                                          cGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCa                                                                                                                                                                >  2:594672/1‑126 (MQ=255)                                                                                                                                                               aTGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGCTTGCTCAATGGGCGCGGCAGGCGGCGTTGTTGTAGGGGCCAGAGTGGCGCAc                                               >  2:351451/1‑234 (MQ=255)                                                                                                                                                                tGGCCACATAAAGCAACTTGTCCACACTGTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGc                                                                                                   <  1:712450/181‑1 (MQ=255)                                                                                                                                                                    cacaTAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGCTTGCTCAATGGGCGCGGCAGGCGGCGTTGTTGTAGGGGCCAGAGTGGCGCACCCAGCCt                                        <  1:351452/236‑1 (MQ=255)                                                                                                                                                                         aaaGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCTCGCTGTCACTGGGCAGGTTCCAAGCac                                                                                                                                                                                                          >  2:85759/1‑68 (MQ=255)                                                                                                                                                                         aaaGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCa                                                                                                                                                                >  2:373883/1‑111 (MQ=255)                                                                                                                                                                         aaaGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCa                                                                                                                                                                <  1:373884/111‑1 (MQ=255)                                                                                                                                                                         aaaGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGGTGTTTGCCGCCTGAgggc                                                                                                        >  2:173874/1‑165 (MQ=255)                                                                                                                                                                            gCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAGTTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCaaac                                                                                                     <  1:537639/167‑3 (MQ=255)                                                                                                                                                                                cTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTgcc                                                                                                                  <  1:320691/150‑1 (MQ=255)                                                                                                                                                                                  tGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGCTTGCTCAATGGGCGCGGCAGGCGGCGTTGTTGTAGGGGCCAGAGTGGCGCACCCAGCCTTTGCCCGGGTtgtg                          <  1:452925/236‑1 (MQ=255)                                                                                                                                                                                         aGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGCTTGCTCAATGGGCGCGGCAGGCGGCGTTGTTGTAGGGGCCAGAGTGgcgc                                                 <  1:42291/206‑1 (MQ=255)                                                                                                                                                                                           tttCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTg                                                                                                                                                                                                                          <  1:572024/35‑1 (MQ=255)                                                                                                                                                                                                        cgTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAg                                                                                                                                                                                                             >  2:572023/1‑35 (MQ=255)                                                                                                                                                                                                           aGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGCTTGCTCAATGGGCGCGGCAGGCGGCGTTGTTGTAGGGGCCAGAGTGGCGCACCCAGCCTTTGCCCGGGTTGTGGGCCGAACACAGGTAGCGGCCGGt  <  1:627946/235‑1 (MQ=255)                                                                                                                                                                                                              |                                                                                                                                                                                                                                        GGCGCTCGGTCATGGCGAATGCACGCGCCGGAAAGCTGTCACCGAACACCGGCATCGAGCGGGCCTGCTCCAGGTCGCGCTGAAAACCGTTGGTGGAAATGTTCGCCAGGTTGTTGGCGTGGGCCTTCTGCGCCAGCGCGTTCTGGCTGGCGCCGGTCATGGCCACATAAAGCAACTTGTCCACAGTTTCTCCTCTGCGCGTAGCTGCCGCGCTGTCACTGGGCAGGTTCCAAGCAATAATTGAACCAAGTCTGAAACACCCGGTTTACGGGGCTTTCAGCGCGGCAAGGGGCAATAACCGTCAGTTTGTCGGCGGATGTTTGCCGCCTGCGGCAAGGGCTTGCTCAATGGGCGCGGCAGGCGGCGTTGTTGTAGGGGCCAGAGTGGCGCACCCAGCCTTTGCCCGGGTTGTGGGCCGAACACAGGTAGCGGCCGGT  >  AE015451/4980026‑4980462

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ 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.