New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	4 (0.120)	12 (0.470)	11/128	1.0	77.0%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	4 (0.160)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment

GCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTT  >  NC_000913/1209541‑1209690                                                                               |                                                                        taaccggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGt                                                                       <  2:238881‑M2/3‑1 (MQ=255) gccagccTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGt                                                                       <  2:239063/81‑1 (MQ=255)   accggtatagctatgaaaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGtt                                                                      <  2:238880‑M2/4‑1 (MQ=255)                   aaccggtgcgtcctaatgtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGaaa                                                      >  2:239094‑M2/61‑80 (MQ=255)                    ggCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAAt                                                     >  2:239099/1‑80 (MQ=255)                                    gtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGcat                                     >  2:239109‑M2/44‑80 (MQ=255)                                    gtagccgttgctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGcat                                     >  1:239106‑M2/44‑80 (MQ=255)                                              ctgcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCtt                          <  2:238875‑M2/48‑1 (MQ=255)                                                gcattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCttt                         >  1:239105‑M2/32‑80 (MQ=255)                                                aCAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCttt                         >  1:239107/1‑80 (MQ=255)                                                 cattgagttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCtttt                        <  2:238877‑M2/50‑1 (MQ=255)                                                      agttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAgg                  <  1:238879‑M2/56‑1 (MQ=255)                                                      agttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAg                   <  1:238874‑M2/55‑1 (MQ=255)                                                       gttttgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAggg                 >  2:239104‑M2/25‑81 (MQ=255)                                                           tgctccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGa              <  1:239076‑M2/60‑1 (MQ=255)                                                             agCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGAttt           <  2:239077/81‑1 (MQ=255)                                                               ccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTaa         >  2:239101‑M2/17‑81 (MQ=255)                                                               ccttctcccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTaa         >  2:239114‑M2/17‑81 (MQ=255)                                                                      ccaaaccaaCGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCtt  <  1:239078‑M2/72‑1 (MQ=255)                                                                               |                                                                        GCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTTACCAGGGGGATTTAACATGCTT  >  NC_000913/1209541‑1209690

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