New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	2065000 =	28 (0.700)	3 (0.080)	3/304	NT	8.3%	intergenic (+1/‑20)	isrC/flu	novel sRNA, CP4‑44; putative prophage remnant/CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
	?	CP009273	2065385 =	39 (0.990)					coding (366/3120 nt)	flu	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

CTGATGGTCATTCCGTTGGTCGTACCGAAGACAATCTGGTTGTCATGATTTGCCAGTGTTCCGCCGTTCACGGTTTCTCCCGGGTGCACAACGATGTCAGCAGCCAGCACCGGGAGTGACGTGACTGCGGCAAGAGACAGTGCAACCGCCACACCGCCACGTTTACCCCGTGCGCGGGCCAGTTCGGAGGCAACCACGAAAGCGCCCGTCATGTGATTCCATACCAGCCTGTAGCAGGTATTCAGATGTCGTTTCATCAGCTTTTCCTTAGATTGAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/2065276‑2065000 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gagAGTGAACCCCGGTGGAAGTGTCTCAGACACGGTTATCAGTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGG  >  CP009273/2065385‑2065545                                                                                                                                                                                                                                                                                                                                                                                                                                                        cgtagGGTCTTTCCGTTGGGCGTACCGAAGACAATCTGGTTGTCATGATTTGCCAGTGTTCCGCCGTTCACGGTTTCTCCCGGGTGCACAACGATGTCAGCAGCCAGCACCGGGAGTGACGTGACTGCGGCAAGAGACAGTGCAACCGCCACACCGCCACGTTTACCCCGTGCGCGGGCCAGTTCGGAGGCAACCACGAAAGCGCCCGTCATGTGATTCCATACCAGCCTGTAGCAGGTATTCAGATGTCGTTTCATCAGCTTTTCCTTAGATTG                                                                                                                                                                     <  1:237019/270‑1                                                                                                                                                                    TACCCCTTGCGCGGCCCAGTTCGGAGGCAACCACGAAAGCGCCCGTCATGTGATTCCATACCAGCCTGTAGCAGGTATTCAGATGTCGTTTCATCAGCTTTTCCTTAGATTGGGAGTGAACCCCGGTGGAAGTGTCTCAGACACGGTTATCAGTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGG  <  1:382474/275‑1                                                                                                                                                                                                                                                  TCAGATGTCGTTTCATCAGCTTTTCCTTAGATTGAGAGTGAACCCCGGTGGAAGTGTCTCAGACACGGTTATCAGTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACAC                                                                                  >  1:65319/1‑117                                                                                                                                                                                                                                                      ATGTCGTTTCATCAGCTTTTCCTTAGATTGAGAGTGAACCCCGGTGGAAGTGTCTCAGACACGGTTATCAGTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACG                                                                              <  2:65318/117‑1                                                                                                                                                                                                                                                                                                                                                                                                                                                        CTGATGGTCATTCCGTTGGTCGTACCGAAGACAATCTGGTTGTCATGATTTGCCAGTGTTCCGCCGTTCACGGTTTCTCCCGGGTGCACAACGATGTCAGCAGCCAGCACCGGGAGTGACGTGACTGCGGCAAGAGACAGTGCAACCGCCACACCGCCACGTTTACCCCGTGCGCGGGCCAGTTCGGAGGCAACCACGAAAGCGCCCGTCATGTGATTCCATACCAGCCTGTAGCAGGTATTCAGATGTCGTTTCATCAGCTTTTCCTTAGATTGAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/2065276‑2065000 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gagAGTGAACCCCGGTGGAAGTGTCTCAGACACGGTTATCAGTGCCGGAGGCGGACAGAGCCTTCAGGGACGGGCTGTGAACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGG  >  CP009273/2065385‑2065545

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ 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.