New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2080720 =	43 (1.160)	3 (0.090)	3/244	NT	6.8%	intergenic (‑188/+55)	USA300HOU_1938/USA300HOU_1939	hypothetical protein/hypothetical protein
	?	CP000730	2080773 =	41 (1.170)					intergenic (‑241/+2)	USA300HOU_1938/USA300HOU_1939	hypothetical protein/hypothetical protein

ATAAGTTATTGAATTTCAAAAGTTCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTC  >  CP000730/2080580‑2080858                                                                                                                                             |                                                                                                                                                   cttcagtatgatactttagtcgaacggaggtgtagtgtaatgatgtggtggcaagaagggatgatgacacttattacaggtggcttactaattatttttcgactttggttagaactgaaatggaaaaataaaaaatgatcc                                                                                                                                                    <  1:69568‑M1/1‑1 (MQ=255) ataaGTTATTGAATTTCAAAAGTTCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTAtac                                                                                                                                                    >  1:439851/1‑141 (MQ=255)   tcagtatgatactttagtcgaacggaggtgtagtgtaatgatgtggtggcaagaagggatgatgacacttattacaggtggcttactaattatttttcgactttggttagaactgaaatggaaaaataaaaaatgatcctt                                                                                                                                                  <  2:433847‑M1/3‑2 (MQ=255)    cagtatgatactttagtcgaacggaggtgtagtgtaatgatgtggtggcaagaagggatgatgacacttattacaggtggcttactaattatttttcgactttggttagaactgaaatggaaaaataaaaaatgatcCTac                                                                                                                                                 <  1:112743‑M1/4‑1 (MQ=255)     gTTATTGAATTTCAAAAGTTCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTaca                                                                                                                                                <  2:63985/141‑1 (MQ=255)          tGAATTTCAAAAGTTCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑Acc                                                                                                                                   >  1:433847/1‑141 (MQ=255)          tGAATTTCAAAAGTTCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑Acc                                                                                                                                   <  1:134262/141‑1 (MQ=255)                tCAAAAGTTCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGt                                                                                                                             <  1:81125/141‑1 (MQ=255)                     aGTTCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGt                                                                                                                        >  1:343784/1‑141 (MQ=255)                     aGTTCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGt                                                                                                                        >  2:349855/1‑141 (MQ=255)                       ttCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTAc                                                                                                                      >  1:85529/1‑141 (MQ=255)                           aGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACcagc                                                                                                                  <  1:47799/141‑1 (MQ=255)                            ggTAGTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACcagca                                                                                                                 >  2:134138/1‑141 (MQ=255)                                     cACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTgggg                                                                                                        >  1:40069/1‑141 (MQ=255)                                      aCTTTCAACTAAAATAGCGCAACAAGACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGt                                                                                                       <  2:426155/141‑1 (MQ=255)                                       aaatgatatAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCCAGTCTGGTACCAGCAGACTTGGGGtt                                                                                                      <  2:46038/133‑1 (MQ=255)                                        tttCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGtta                                                                                                     <  2:370595/141‑1 (MQ=255)                                          gatgtggtggcaagaagggatgatgacacttattacaggtggcttactaattatttttcgactttggttagaactgaaatggaaaaataaaaaatgatcCTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGttatt                                                                                                   <  1:64188‑M1/42‑1 (MQ=255)                                                          aacaaAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGTTCa                                                                                   >  2:407686/1‑141 (MQ=255)                                                          aacaaAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCa                                                                                   >  1:346843/1‑141 (MQ=255)                                                           ggatgatgacacttattacaggtggcttactaattatttttcgactttggttagaactgaaatggaaaaataaaaaatgatcCTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCAt                                                                                  >  2:64188‑M1/83‑141 (MQ=255)                                                                atgacacttattacaggtggcttcctaattatttttcgactttggttagaactgaaatggaaaaataaaaaatgatcCTACACACATAAATAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGAt                                                                                     >  1:185945‑M1/78‑141 (MQ=255)                                                                   aTTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTAtt                                                                          >  1:64151/1‑141 (MQ=255)                                                                       aatccaACTGATTATTGATTGCGATATATTGTCTTCAAAGATACTACACAAGTGTATCGACAGAATTAGACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCGGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGCTCATTTTTTAtttttt                                                                      >  2:152879/1‑140 (MQ=255)                                                                        atcaaAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTcc                                                                     <  2:201464/141‑1 (MQ=255)                                                                        atcaaAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTcc                                                                     <  2:201490/141‑1 (MQ=255)                                                                                gATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCTATTTCAGt                                                             >  2:171154/1‑141 (MQ=255)                                                                                  ttattGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTc                                                           <  1:107155/141‑1 (MQ=255)                                                                                   tattGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCt                                                          >  1:123526/1‑141 (MQ=255)                                                                                   tattGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCt                                                          <  1:192477/141‑1 (MQ=255)                                                                                   tattGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCt                                                          <  1:192593/141‑1 (MQ=255)                                                                                    tttgaatgCGAAATCTTTTGTTCAATGATATTATTTAAGGGTATCCACAGAATTCTACTCCAGA‑‑‑‑‑‑‑‑ACTCCCAGTCTGCTACCAGCAGACTTTGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTa                                                         <  2:307912/140‑1 (MQ=255)                                                                                     ttgattgCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTaa                                                        >  1:82508/1‑141 (MQ=255)                                                                                           gCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAg                                                  >  1:426476/1‑141 (MQ=255)                                                                                             gATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTc                                                <  1:278768/141‑1 (MQ=255)                                                                                                    tgtgTTCAATGATATTATGTAAGGGTATCCACAGAATTGTAGTAGACA‑‑‑‑‑‑‑‑GGCTGGAGGCGGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGAACATTTTTTATTTTTCCATTTCAGTTCTATCCAAAGTCGAAAaat                                         <  2:427562/141‑1 (MQ=255)                                                                                                     gtgtTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTTGGGTTATTTATGTGTGTAGGATAATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTGGAAAaata                                        >  2:39843/1‑141 (MQ=255)                                                                                                         acAAAGAAATTATTTAAGTATATCCACAAAAATATAAAACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTAAGTGTGTAAAAAAATTTATTAATATTCCATTTAAGTTAAAAAAAAAAAAAAAAAATAATTa                                    <  2:148713/140‑1 (MQ=255)                                                                                                            aTGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTa                                 >  1:251466/1‑141 (MQ=255)                                                                                                                  ttattTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCAc                           <  1:306207/141‑1 (MQ=255)                                                                                                                    attTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTTTATTTTTGTTTTATCTAAAGTCGAAAAATAATTAGTAAGCCATCt                         >  2:355220/1‑141 (MQ=255)                                                                                                                    attTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTACCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCt                         <  1:377018/141‑1 (MQ=255)                                                                                                                    attTAAAAGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAAAAAAAAAAAAAAAATAATTAGTAAGCCACCt                         <  2:372277/141‑1 (MQ=255)                                                                                                                       tAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGta                      <  2:289770/141‑1 (MQ=255)                                                                                                                        aaGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGtaa                     >  2:57940/1‑141 (MQ=255)                                                                                                                          gtgtATCCACAGCATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGAGTTATTGATGTGTGTAGGCTCATTTTTTATTTTCCCCTTTCAGTTCTAACCAGAGTCGAAAAATAATTAGTAAGCCACCTGtaaca                   <  2:158689/141‑3 (MQ=255)                                                                                                                          gtgtATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGtaata                   <  2:158688/141‑1 (MQ=255)                                                                                                                          gggtATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACACCAAGTCGGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAACTAATTAGTTAGCCACCTGtaatc                   <  2:19261/139‑2 (MQ=255)                                                                                                                            ttATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAAAAAAAAAAAAAAAATAATTAGTAAGCCACCTGTAATAAg                 <  2:33218/140‑1 (MQ=255)                                                                                                                            gtATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATTATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAATCCACCTGTAATAAg                 >  2:69468/1‑141 (MQ=255)                                                                                                                                      aaTTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCTATTTTAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTatcatcatc       >  2:128707/1‑141 (MQ=255)                                                                                                                                           tactacACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCcttc  <  2:21329/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                   ATAAGTTATTGAATTTCAAAAGTTCAAGGTACTAATCACTTTCAACTAAAATAGCGCAACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTC  >  CP000730/2080580‑2080858

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.