New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	46 (1.140)	4 (0.110)	4/226	NT	11.3%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	23 (0.650)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

GTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCGT  >  USA300TCH1516_ALE/909602‑909875                                                                                                                                           |                                                                                                                                        gttgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAtt                                                                                                                                       <  1:242871‑M2/141‑3 (MQ=255) gttgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAtt                                                                                                                                       <  1:473646‑M2/141‑3 (MQ=255)          aaaataaaaaaaagggcatAATTTTGAAACAAAGGTCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTTATAATCTGGCTAAttattcctgct                                                                                                                              >  2:25169‑M2/7‑130 (MQ=255)          aaaaaaaaaaaaagggcatAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgct                                                                                                                              >  2:190492‑M2/7‑130 (MQ=255)                    aaaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAGTGCATATATAACAATGATTTGATTGCGCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataactca                                                                                                                    <  2:429399‑M2/141‑22 (MQ=255)                     aaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCat                                                                                                                   >  1:473777/1‑141 (MQ=255)                      aGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCata                                                                                                                  <  2:220822/141‑1 (MQ=255)                       gggCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATGatgt                                                                                                                 >  1:64770/1‑139 (MQ=255)                                                            ataaATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCtttttct                                                                            >  1:149353/1‑139 (MQ=255)                                                                        gAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAACCAggca                                                                >  2:452249/1‑139 (MQ=255)                                                                                    aaTGCATATATAACAATGTTTTGATTGCACTTGAACTTCCTTGATAATCTGGCTAATTATTACTGCTAAATCAATCATATTAATGTCTCAGTAAAGTCATGTTGCTTACATTTTTAATTTACACAGGTATTTATATGatat                                                    >  2:183922/1‑141 (MQ=255)                                                                                     aTGCATATATAACAATGTTTTGATTGCCCTTGTACTTCCTTGATAATCTGGCTAAttattcctgataaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaa                                                   >  2:13449‑M2/1‑55 (MQ=255)                                                                                          tatagaACGATGTTTTCCTTTCTCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGTTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGa                                              <  2:452963/141‑1 (MQ=255)                                                                                              taACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaagggactatttttgtggtattgaaaataaaaaagggcac                                          <  2:94957‑M2/141‑96 (MQ=255)                                                                                                   aTGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGc                                     <  2:32031/141‑1 (MQ=255)                                                                                                        ttGATTGCCCTTGTACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTTGGAATGAGATGCTATTa                                >  1:102598/1‑141 (MQ=255)                                                                                                        ttGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattcaataaaaatacactttaataacaacgattaagggtttatttttgtggtattgaaaataaaaaagagcacaaaagttgca                                <  2:129128‑M2/141‑106 (MQ=255)                                                                                                          gATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagatcacaaaaggggcagt                              <  1:183248‑M2/141‑108 (MQ=255)                                                                                                            ttGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATAAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACggt                            >  1:253160/1‑140 (MQ=255)                                                                                                             tGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACACGTCTTTCTATGTTATTTATGACTGAGCTGATATTACggtt                           >  1:121253/1‑139 (MQ=255)                                                                                                               cccTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATTACTACAGTGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGATATGCTATTACGGATaa                         >  2:204662/1‑141 (MQ=255)                                                                                                                ccTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATaaa                        <  2:165344/141‑1 (MQ=255)                                                                                                                ccTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATaaa                        <  2:165238/141‑1 (MQ=255)                                                                                                                  ttGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGt                      <  1:75713/141‑1 (MQ=255)                                                                                                                  ttGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGt                      <  1:140281/141‑1 (MQ=255)                                                                                                                    gAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAATTaa                    >  2:157221/1‑141 (MQ=255)                                                                                                                      aCTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAACGTaaaa                  >  2:360151/1‑141 (MQ=255)                                                                                                                       ctgccTTGATATTCTAGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGGAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAAt                 <  2:5476/138‑1 (MQ=255)                                                                                                                       cTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAAt                 >  2:356541/1‑141 (MQ=255)                                                                                                                             tGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCtata           >  1:184047/1‑141 (MQ=255)                                                                                                                             tGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTCAAGTCGCAAGACTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCtata           >  1:496252/1‑141 (MQ=255)                                                                                                                               aTAATCTGGCTAATGATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATatg         <  1:478668/141‑1 (MQ=255)                                                                                                                                 gaTCGGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATatgca       >  2:88029/2‑141 (MQ=255)                                                                                                                                      ggCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATatgcatgctt  >  2:246587/1‑139 (MQ=255)                                                                                                                                           |                                                                                                                                        GTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCGT  >  USA300TCH1516_ALE/909602‑909875

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.