New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	12 (0.410)	8 (0.320)	8/226	NT	27.4%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	32 (1.270)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

GGTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCGT  >  USA300TCH1516_ALE/909601‑909875                                                                                                                                            |                                                                                                                                        ggTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAt                                                                                                                                        >  1:116564‑M2/1‑140 (MQ=255) ggTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAt                                                                                                                                        >  1:162472‑M2/1‑140 (MQ=255)   ttgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAtta                                                                                                                                      <  1:60099‑M2/141‑4 (MQ=255)    tgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttat                                                                                                                                     >  1:20006‑M2/1‑137 (MQ=255)          cAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgc                                                                                                                               >  1:567648‑M2/1‑131 (MQ=255)           aaGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAGTGCATATGTAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgct                                                                                                                              <  1:251209‑M2/141‑12 (MQ=255)           aaGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgct                                                                                                                              <  1:598037‑M2/141‑12 (MQ=255)            aGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgcta                                                                                                                             >  1:122199‑M2/1‑129 (MQ=255)              ggCAAAAAAAGGGCGTAATTTTGAAACAAAGGGCAAGGGTATGACTAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaa                                                                                                                           <  1:367905‑M2/141‑15 (MQ=255)                    aaaaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATc                                                                                                                     >  1:101766/1‑141 (MQ=255)                      aaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCat                                                                                                                   >  1:591691/1‑141 (MQ=255)                       aGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaa                                                                                                                  <  1:237336‑M2/141‑24 (MQ=255)                       aGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCata                                                                                                                  <  1:4221/141‑1 (MQ=255)                         ggCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATAtt                                                                                                                <  1:105482/141‑1 (MQ=255)                          gCATAATTTTGAAACAAAGGGCAAGGGTATGACAAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTa                                                                                                               <  1:82925/141‑1 (MQ=255)                          gCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATCAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTACTTATTCCTGCTAAATAAATCATATTa                                                                                                               >  1:412886/1‑141 (MQ=255)                          gCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGGCAGTGGGCTTCCTTGATAATATGGCCAATTGTTCCTGCTAAATAAATCATATTa                                                                                                               >  1:89118/1‑141 (MQ=255)                           aaTAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTaa                                                                                                              <  1:195121/140‑1 (MQ=255)                               aTTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGCTAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGc                                                                                                          <  1:361103/141‑1 (MQ=255)                                           aGGGCAAGGGTATGAATAATAAACTATCGTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGa                                                                                              <  1:665/141‑1 (MQ=255)                                                aatggTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTg                                                                                         <  1:281385/138‑1 (MQ=255)                                                aaGGGGATGAATAATAAATTATCCTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGCTAATCTGTCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTg                                                                                         <  1:281389/141‑1 (MQ=255)                                                       tGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCt                                                                                  <  1:257151/141‑1 (MQ=255)                                                        gAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCtt                                                                                 <  1:38430/141‑1 (MQ=255)                                                             ataaATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaagggg                                                                            <  1:275969‑M2/141‑62 (MQ=255)                                                                  ttATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAGTCTGGCTAATTATTCCTTCTAAATAAATCATTTTTATGGCTCAGTAACGTGAGGTTTCTTGGCTTtttaatttaa                                                                       >  1:471738/1‑141 (MQ=255)                                                                  ttATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTtttaatttaa                                                                       <  1:363971/141‑1 (MQ=255)                                                                   tATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTaaa                                                                      <  1:249310/141‑1 (MQ=255)                                                                          aaaaTTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggt                                                               >  1:586371‑M2/1‑67 (MQ=255)                                                                          aaaaTTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTAt                                                               >  1:404938/1‑141 (MQ=255)                                                                             aTTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCGTATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTta                                                            <  1:359005/141‑1 (MQ=255)                                                                             aTTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTta                                                            <  1:526796/141‑1 (MQ=255)                                                                               tttATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggtgatttttgtggtattga                                                          <  1:639523‑M2/141‑80 (MQ=255)                                                                               tttATAAATGCATACATACCAATGTTTTGCTTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTtata                                                          <  1:182077/141‑1 (MQ=255)                                                                                   taAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTGTTAATTTAAACAGGTGATtataggta                                                      >  1:240194/1‑137 (MQ=255)                                                                                    aaaTGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGata                                                     <  1:583216/141‑1 (MQ=255)                                                                                        gCATATATACCAATGTGTTGATTGCCCTTGAACCTCCTTGATAATCTGGCCAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTa                                                 <  1:184738/141‑1 (MQ=255)                                                                                          atatatAACAATGTTTTGATTGCCCTTGAACTTTCTAGATAATCTGGCTAAATATTCCTGCTAAATAAATCATATTCATGGCTCAGTAACGAGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAgg                                               <  1:141094/141‑1 (MQ=255)                                                                                                aaCAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcaca                                         >  1:104848‑M2/1‑45 (MQ=255)                                                                                                  aaatGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaa                                       >  1:250043‑M2/2‑43 (MQ=255)                                                                                                      gTTTTGATTGCTCTCGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTa                                   <  1:597714/141‑1 (MQ=255)                                                                                                      gTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTa                                   >  1:344297/1‑141 (MQ=255)                                                                                                         ttGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaaaggggca                                <  1:387677‑M2/141‑106 (MQ=255)                                                                                                           gATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACg                              >  1:623768/1‑141 (MQ=255)                                                                                                            aTTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaaaagcgcaaaaggggtagta                             <  1:8647‑M2/141‑109 (MQ=255)                                                                                                                 ccTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATaaa                        <  1:270951/141‑1 (MQ=255)                                                                                                                   ttGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATCAATGGCTCAGTAACGTGATGTTGCTGGGCTTCTTAATTTAAACAGGTATTTATATGATATTTAGGAATGATATGCTATTACGGATAAAGt                      <  1:403337/141‑1 (MQ=255)                                                                                                                              tGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAATTCCtata           <  1:423125/141‑1 (MQ=255)                                                                                                                                 tAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATatgc        >  1:554987/1‑141 (MQ=255)                                                                                                                                      tGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCg   >  1:256872/1‑141 (MQ=255)                                                                                                                                       ggCTAATTATTCCTGATAAATAAATCATATTAATGGCTCAGTAGCGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAAGAATGAGATGCTATTACGGATAAAGAAAAATCCTATATGCATGCGt  <  1:472903/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                        GGTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCGT  >  USA300TCH1516_ALE/909601‑909875

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.