New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	= 4945203	41 (1.000)	5 (0.130)	5/318	NT	13.2%	intergenic (+563/+235)	PP_5673/flhB	putative D‑alanine‑‑D‑alanine ligase/flagellin export apparatus, substrate specificity protein
	?	AE015451	4945621 =	27 (0.700)					coding (960/1143 nt)	flhB	flagellin export apparatus, substrate specificity protein

CTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451/4945066‑4945203 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcccgcgcCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATACGTT  >  AE015451/4945621‑4945853                                                                                                                                                                                                                                                                                                                                                                                     CTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACG                                                                                                                                            >  2:275801/1‑233         GCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCgc                                                                                                                                                                                                                                               >  1:251834/1‑124         GCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCgc                                                                                                                                                                                                                                               <  2:251833/126‑3               CTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCG                                                                                                                                                                                                                                              <  1:210031/121‑1               CTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCG                                                                                                                                                                                                                                              >  2:210030/1‑121                     CGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGTTGTTGTGCTCCACGCCA                                                                                                                                                                                                >  2:671034/1‑161                                                                                            TTCGCCGTGAGGTTGTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCA                                                                                                                                                                                          <  2:195705/96‑1                                                                                                                  CTGTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCG                        <  1:388077/236‑1                                                                                                                    GTGAGATCGAGCGCCGCCCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCG                                     >  1:244831/1‑221                                                                                                                                     CCGCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATAC     >  1:616920/1‑236                                                                                                                                       GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATACGT   >  1:726911/1‑236                                                                                                                                       GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGA         >  1:746909/1‑230                                                                                                                                       GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGA         <  2:746908/230‑1                                                                                                                                       GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATC                                             <  1:231437/194‑1                                                                                                                                       GCGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATC                                             >  2:231436/1‑194                                                                                                                                        CGCCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATACGTT  <  1:446846/236‑1                                                                                                                                                                                                                                                                                                                                                                                     CTCTTGATGCAAAACTTTGACGCCCAGGGGGCGCCTGCGGCTGGCATTGCTAGAAGCTTTCCAACTTTGTGATCTGCTGTGAATCGGGGTGTTCGCCGTGAGGTTTTTGTCGCCTGTGAGATCGAGCGCCGCCCGCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451/4945066‑4945203 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgcccgcgcCAGCGCCGGCGATTCGAGGATCTGGATGTTGTGCTCCACGCCAATTTCACGAATCTTCAACGCCATGAAATCGCTACCCTTGGCCAGCAGCAACGGCGCCGCACCGCCTTTCTCCGGGTCGTATTGCAAAGCCACCGCATAATGCGTCGGGTTGGTGATGATCACATCTGCATCCGGTACCGCCGCCATCATGCGCCGCTGCGACACCTCGCGCTGCAGTTGGCGAATACGTT  >  AE015451/4945621‑4945853

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ 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.