New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1443583	78 (0.790)	4 (0.040)	3/248	NT	7.2%	intergenic (‑156/+197)	USA300HOU_1341/brnQ2	IS1272 transposase/LIVCS family branched chain amino acid:cation symporter
	?	CP000730	2317554 =	28 (0.290)					intergenic (+207/+1909)	rhbC/asp23	possible Iuc family aerobactin synthesis protein/alkaline shock protein 23

ATGAGAGAATAATACATTTTCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAAGAC  >  CP000730/2317414‑2317692                                                                                                                                             |                                                                                                                                           aTGAGAGAATAATACATTTTCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACt                                                                                                                                            <  2:786298/141‑1 (MQ=255)  tagtttagtagtatttattaaattatacgaagggatccaacacagaaaatttattttattgaattttacatttatgtgcaagttgggcaaagtgtcttatttttttaaagtatttcaaagtaaaattacacgttaatacta                                                                                                                                           <  1:541518‑M2/2‑2 (MQ=255)  tGAGAGAATAATACATTTTCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTAGACAATACtt                                                                                                                                           <  1:1050027/141‑1 (MQ=255)     gagaATAATACATTTTCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGt                                                                                                                                        >  1:531356/1‑141 (MQ=255)     gagaATAAGGCAGTGTGCAGAGTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTCCTGCTGTTCTCTATTTATACAATACTTCGt                                                                                                                                        <  2:1072207/141‑1 (MQ=17)     aagaATAATACATTTTCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGt                                                                                                                                        <  2:381664/140‑1 (MQ=255)       gaATAATACATTTTCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTAt                                                                                                                                      <  1:745677/141‑1 (MQ=255)         gtagtatttattaaattatacgaagggatccaacacagaaaatttattttattgaattttacatttatgtgcaagttgggcaaagtgtcttatttttttaaagtatttcaaagtaaaattacacgttaatacTACGTatta                                                                                                                                    >  2:366067‑M2/133‑140 (MQ=255)         ataataCATTTTCCATATTCAAATTATTAAAAATGACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACTATACTTCGTATTg                                                                                                                                    <  2:523918/141‑1 (MQ=255)         ataataCATTTTCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTg                                                                                                                                    <  2:926911/141‑1 (MQ=255)                 ttttCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCtt                                                                                                                            >  2:1020304/1‑141 (MQ=255)                    tCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGc                                                                                                                         <  1:434130/141‑1 (MQ=255)                     ccATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCt                                                                                                                        >  1:322279/1‑141 (MQ=255)                      cATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGt                                                                                                                                        >  2:875645/1‑124 (MQ=255)                      cATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGt                                                                                                                                        <  1:875645/124‑1 (MQ=255)                      cATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCtt                                                                                                                       >  2:352783/1‑141 (MQ=255)                      aaaatTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCtt                                                                                                                       >  2:393685/4‑141 (MQ=255)                         atTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTcc                                                                                                                    <  2:964270/141‑1 (MQ=255)                             aaaTTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAgg                                                                                                                <  2:317092/141‑1 (MQ=255)                                ttattaAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTg                                                                                                             >  2:615511/1‑141 (MQ=255)                                    taAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGt                                                                                                         <  2:1015793/141‑1 (MQ=255)                                    aaaaaaTCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGt                                                                                                         <  2:78778/140‑1 (MQ=255)                                     aaaaaTCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGtc                                                                                                        <  1:320454/141‑1 (MQ=255)                                      aaaaTCACAAAAAACAGGCTGGGACATACATCCCTAAAAAAACAGCACTAAGATAATTCTCACTTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGATGCCGtct                                                                                                       >  2:213737/1‑141 (MQ=14)                                             caAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTc                                                                                                >  1:562705/1‑141 (MQ=35)                                             caAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTc                                                                                                <  1:278207/141‑1 (MQ=35)                                              aaaaaaCAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCg                                                                                               >  1:756437/1‑141 (MQ=34)                                               aaaaaCAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAAATAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCgg                                                                                              >  2:718321/1‑141 (MQ=18)                                                   aCAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCtt                                                                                          >  2:637693/1‑141 (MQ=32)                                                    cAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTc                                                                                         >  2:48386/1‑141 (MQ=32)                                                       gCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGAc                                                                                      >  2:445713/1‑141 (MQ=31)                                                       gCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACGGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGAc                                                                                      >  2:944112/1‑141 (MQ=14)                                                        cTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACt                                                                                     >  1:389375/1‑141 (MQ=11)                                                                                    ttgggcaaagtgtcttatttttttaaagtatttcaaagtaaaattacatgttaatacGTAGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCAt                                                         <  2:1155817‑M2/84‑1 (MQ=255)                                                                                              tgtcttatttttttaaagtatttcaaagtaaaattacacgttaatacTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACg                                               <  1:949216‑M2/94‑1 (MQ=255)                                                                                                tcttatttttttaaagtatttcaaagtaaaattacacgttaatacTTCGTATTGAATGGCTTCGCTTTCCTTGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTa                                             <  1:813451‑M2/96‑1 (MQ=255)                                                                                                                               tATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACtttt              <  1:225699/141‑1 (MQ=11)                                                                                                                                aTTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTa             >  1:459252/1‑141 (MQ=31)                                                                                                                                aTTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTa             >  2:845619/1‑141 (MQ=31)                                                                                                                                 tttATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTaa            <  2:178081/141‑1 (MQ=32)                                                                                                                                      aCAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAAt       >  2:1170515/1‑141 (MQ=32)                                                                                                                                       cAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATa      <  2:1008423/141‑1 (MQ=32)                                                                                                                                        aatacTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATaa     <  2:453052‑M2/136‑1 (MQ=255)                                                                                                                                        aatacTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATaa     >  2:902821‑M2/6‑141 (MQ=255)                                                                                                                                        aatacTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATaa     >  1:112955‑M2/6‑141 (MQ=255)                                                                                                                                         atacTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAAg    <  2:605631‑M2/137‑1 (MQ=255)                                                                                                                                           acTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCgg                                                                                              >  2:388839‑M2/3‑49 (MQ=255)                                                                                                                                           acTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCgg                                                                                              <  1:388839‑M2/47‑1 (MQ=255)                                                                                                                                           acTTCGGATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAAGac  <  2:33147‑M2/139‑1 (MQ=255)                                                                                                                                             |                                                                                                                                           ATGAGAGAATAATACATTTTCCATATTCAAATTATTAAAAATCACAAAAAACAGGCTGGGACATAAATCCCTAAAAAAACAGCAGTAAGATAATTTTCAATTAGAAAATATCTTACTGCTGTTCTCTATTTATACAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAAGAC  >  CP000730/2317414‑2317692

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.