New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 4945203	62 (0.720)	8 (0.100)	8/338	NT	9.5%	intergenic (+563/+235)	PP_5673/flhB	putative D‑alanine‑‑D‑alanine ligase/flagellin export apparatus, substrate specificity protein
	?	AE015451	4945621 =	93 (1.140)					coding (960/1143 nt)	flhB	flagellin export apparatus, substrate specificity protein

CACCCAGGTTGCCCCGGCCGAGCCCGGCCAGGTTGTTGCGGGCGTTGCTGATTAACTGAGTGCGATCCACCGCGAGTCCTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451/4944988‑4945203 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcccgcgcCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATACGTT  >  AE015451/4945621‑4945853                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CACCCAGGTTGCCCCGGCCGAGCCCGGCCAGGTTGTTGCGGGCGTTGCTGATTAACTGAGTGCGATCCACCGCGAGTCCTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGA                                                                                                                                                                                                                       >  1:240629/1‑236    CCAGGTTGCCCCGGCCGAGCCCGGCCAGGTTGTTGCGGGCGTTGCTGATTAACTGAGTGCGATCCACCGCGAGTCCTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCC                                                                                                                                                                                                                                                   <  1:1311659/205‑1          TGCCCCGGCCGAGCCCGGCCAGGTTGTTGCGGGCGTTGCTGATTAACTGAGTGCGATCCACCGCGAGTCCTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCC                                                                                                                                                                                                                                                >  1:1123901/1‑202                                       CGGGCGTTGCTGATTAACTGAGTGCGATCCACCGCGAGTCCTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTT                                                                                                                                                                                  <  1:133618/235‑1                                                                           AGTCCTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAA                                                                                                                                                                     <  2:240628/212‑1                                                                                                   CGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCC                                                                                                                                                      <  2:25970/203‑1                                                                                                                                       CTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCG                                                                                                                                         >  2:511201/1‑180                                                                                                                                         TTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGT                                                                               <  1:1077205/236‑1                                                                                                                                                            TGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCCTCC                                                            >  1:190045/1‑236                                                                                                                                                                        TGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGC                                                                                                                                                                                                  >  2:1191667/1‑90                                                                                                                                                                                                                CGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGA         <  1:1135176/235‑1                                                                                                                                                                                                                 GCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAAT       <  1:962893/236‑1                                                                                                                                                                                                                  CCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATA      >  1:1445642/1‑236                                                                                                                                                                                                                   CCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGcc                                                                                       >  2:376547/1‑152                                                                                                                                                                                                                   CCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCATATCTGCATCCGGTAC                                                       >  1:1265523/1‑186                                                                                                                                                                                                                   CCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATAC     >  1:258093/1‑236                                                                                                                                                                                                                   CCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATG                                                                                           <  2:127608/150‑1                                                                                                                                                                                                                   CCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATG                                                                                           >  1:127609/1‑150                                                                                                                                                                                                                    CGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGA         <  1:397736/231‑1                                                                                                                                                                                                                     GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATACGT   >  1:601294/1‑236                                                                                                                                                                                                                     GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATACGT   >  1:1437393/1‑236                                                                                                                                                                                                                     GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATAC     >  2:494968/1‑234                                                                                                                                                                                                                     GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATA      >  2:1324109/1‑233                                                                                                                                                                                                                     GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTG                                  >  2:563106/1‑205                                                                                                                                                                                                                     GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGAGCACATCTGCATCCGGTACCGCAGCCATCATGCGCCGCTGCGACACCTCGCGCTG                   >  2:347090/1‑220                                                                                                                                                                                                                     GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGAGACGCACCGCCGTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGG                                                          >  1:517170/1‑181                                                                                                                                                                                                                       GCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATACGTT  <  1:539010/235‑1                                                                                                                                                                                                                                                                                                                                                                                                                                                                   CACCCAGGTTGCCCCGGCCGAGCCCGGCCAGGTTGTTGCGGGCGTTGCTGATTAACTGAGTGCGATCCACCGCGAGTCCTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451/4944988‑4945203 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcccgcgcCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATACGTT  >  AE015451/4945621‑4945853

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ 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.