New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	273955 =	NA (NA)	43 (1.110)	35/284	0.1	95.6%	intergenic (+1/+146)	ykfC/insH1	CP4‑6 prophage, conserved protein,Phage or Prophage Related/IS5 transposase and trans‑activator
	?	NC_000913	618513 =	2 (0.050)					coding (260/1134 nt)	fepE	regulator of length of O‑antigen component of lipopolysaccharide chains

TGTTAATGACGGCTTTATCTTTCTGGGGCACAGGCTCATTCGCAAACGCAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAT  >  NC_000913/273821‑274091                                                                                                                                       |                                                                                                                                         cgttcaggACGGCTGTATCTGGCTGGGGCACAGGCTCATTCGCAAACGCAGTCGTGATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGc                                                                                                                                  <  2:398590/136‑1 (MQ=255)  gTTAATGACGGCTTTATCTTTCTGGGGCACAGGCTCATTCGCAAACGCAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACCGCACTGTTAGGGAAGGTGCg                                                                                                                                 >  1:510663/1‑143 (MQ=255)   ttAATGACGGCTTTATCTTTCTGGGGCACAGGCTCATTCGCAAACGCAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGa                                                                                                                                <  2:246827/143‑1 (MQ=255)          cGGCTTGAGCGTTCTGGGGCACAGGCTCATTCGCAAACGCAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCg                                                                                                                         <  1:32701/143‑1 (MQ=255)           ggCTTTATCTTTCTGGGGCACAGGCTCATTCGAAAACGCAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGAACCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGGTAGGGAATCAGCGCATAAGCgc                                                                                                                        >  1:146117/1‑142 (MQ=255)                  ggttctgggggCACAGGCTGGTTCCCGAACGGAGTCGCTATGGCGAGATGCGATTGGTCTCAACGGTCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAAtt                                                                                                                 <  1:638820/136‑1 (MQ=255)                  gcgtgcTGGGGCACATGCTCATTCGCAAACTCAGTCGTGATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAAtt                                                                                                                 <  1:488745/138‑1 (MQ=255)                       cTGGGGTACAGGCTCATTCGCAAACGCAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATtcttct                                                                                                            <  1:648390/143‑1 (MQ=255)                                aGGCTCATTCGCAAACGCAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGCATAAGCGGGGAAATTCTTTCCGGCTGAcg                                                                                                   >  1:610231/1‑142 (MQ=255)                                    tCATTCGCGAACGCAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATCAGCGGGGAACTTATTCTCGGCTGGCTCaac                                                                                               >  1:525506/1‑141 (MQ=255)                                                              gagaTGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACCCAATCATTTCATTCCTTCCTGtttcacccc                                                                     >  1:149244/1‑137 (MQ=37)                                                                     gAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTACGGAAGGTGCGCATAAGCGGGGAAAGTCTTCTCGGCTGACACAGTCATTTCATTTCTTCATGTTTGAGCAGAtttttt                                                              >  1:403278/1‑143 (MQ=25)                                                                      agaggTCTCAACGATCCCGCAGGCGAAAGCCAGAAACTTCCCCGCATCGCTGACAGCACTGATATGGAAGATCCGAATAAACGGGGAAATTCCTCTCGGCTGACTCAGTCATTTCAGCTCTGCAAGTCTCAGCCGAtacatgg                                                             >  1:464490/4‑137 (MQ=21)                                                                        tGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTGTTCAGGTTTGAGCCGATTGTTtctc                                                           >  2:247128/1‑143 (MQ=255)                                                                         ggTCCCAACGACCCCGCAGGAGAAAGCCAGAATCTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTcc                                                          <  1:372638/143‑1 (MQ=255)                                                                            ctcAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTGATTTCATTTCTTCGTGTTTGAGCCGATTTTTTCTCCAGt                                                       >  2:555785/1‑143 (MQ=255)                                                                             tcAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTa                                                      >  2:407130/1‑143 (MQ=255)                                                                               aaCGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCCTGTTTGAGCCGATTTTTTCTCCCGTaaa                                                    >  2:448661/1‑143 (MQ=255)                                                                               aaCGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTaaa                                                    >  2:607340/1‑143 (MQ=255)                                                                               aaCGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGATATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATGTCATTTCTTCATGTTTGAGCAGATTTTTTCTCCCGTaaa                                                    >  2:226625/1‑143 (MQ=255)                                                                                          gggAGAAAGCCAGAAGCTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATc                                         <  1:23439/142‑1 (MQ=255)                                                                                            gacacaGCCAGCAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAg                                       <  1:164127/138‑1 (MQ=255)                                                                                             agaAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGc                                      <  2:409018/143‑1 (MQ=255)                                                                                                aaGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCCTGTTTGAGCCGATTTGTCCTCCCGTAAATGCCTTGAATCAGCCTa                                   <  2:529313/143‑1 (MQ=255)                                                                                                  gCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAACTGCCTTGACTCAGCCTAtt                                 >  2:169445/1‑143 (MQ=255)                                                                                                   ccAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTAttt                                >  2:520997/1‑143 (MQ=255)                                                                                                           ttCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCTTTGAATGAGCCTATATAGACCGtt                        >  1:578987/1‑143 (MQ=255)                                                                                                           ttCGCCGCATCGCTGACAGCACTGATATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCCGCCTCTTTAGACCGtt                        >  2:145604/1‑143 (MQ=255)                                                                                                            tCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGttt                       >  1:302141/1‑143 (MQ=255)                                                                                                                                 tGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAt  <  2:640186/143‑1 (MQ=32)                                                                                                                                 tGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAt  >  2:292267/1‑143 (MQ=32)                                                                                                                                       |                                                                                                                                         TGTTAATGACGGCTTTATCTTTCTGGGGCACAGGCTCATTCGCAAACGCAGTCGTTATGGCGAGATGCGAGTGGTCTCAACGATCCCGCAGGAGAAAGCCAGAAACTTCGCCGCATCGCTGACAGCACTGTTATGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAT  >  NC_000913/273821‑274091

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ 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.