New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	10 (0.390)	6 (0.270)	6/226	NT	28.1%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	22 (1.000)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

GTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGC  >  USA300TCH1516_ALE/909605‑909873                                                                                                                                        |                                                                                                                                      gttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttatt                                                                                                                                  <  1:10111‑M2/141‑6 (MQ=255)     tCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctg                                                                                                                              <  1:3551‑M2/141‑10 (MQ=255)       aaGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgct                                                                                                                            <  1:237671‑M2/141‑12 (MQ=255)        aGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgcta                                                                                                                           >  2:131379‑M2/1‑129 (MQ=255)               aaaaaGGGCATAATTTTGAATCAAAGGGCAAGTGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTaaataaat                                                                                                                    <  1:35990/141‑1 (MQ=255)                      gCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccattta                                                                                                             <  2:147605‑M2/141‑27 (MQ=255)                       cATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAACTCATATTaa                                                                                                            >  2:29097/1‑141 (MQ=255)                         tAATTTTGAAACAAAGTGCAAGAGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGCTTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaat                                                                                                          >  2:9178‑M2/1‑112 (MQ=255)                                  aaCAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTaa                                                                                                 >  1:284542/1‑141 (MQ=255)                                       aGGGCAAGGGTATGAATAATAAATTATAGTGTCAATTTTATAAACGCATATAGATCAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGa                                                                                            <  1:43111/141‑1 (MQ=255)                                              gggTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaa                                                                                     <  1:145723‑M2/141‑51 (MQ=255)                                                 tATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTAATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTTATGGCTAAGTAACGTGATGTAACTggg                                                                                  >  2:66131/1‑141 (MQ=255)                                                    gAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCtt                                                                               >  2:44172/1‑141 (MQ=255)                                                      ataataAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCtttt                                                                             <  1:47883/141‑1 (MQ=255)                                                                  cTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAg                                                                 <  1:206285/141‑1 (MQ=255)                                                                       aaaTTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTAATGTTGATGAGCATTTTAATTTAAAAACGTAtt                                                            >  2:240270/1‑141 (MQ=255)                                                                               taAATGATTATATAACAATGTTTTGATTGCCCTTGAACTTACTTGATAATCTGGCTAAttattcctgcgaaataataccaagtaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaat                                                    >  2:11430‑M2/1‑58 (MQ=255)                                                                                     cATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTCTATGATATTTAg                                              <  2:39592/141‑1 (MQ=255)                                                                                         tataAGAGTGTGTTGATTGCCTTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTAAGTAACGTGATGTTGCTGTGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAAt                                          <  2:247080/141‑1 (MQ=255)                                                                                          ataACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATg                                         >  1:100767/1‑141 (MQ=255)                                                                                                aTGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGc                                   <  2:3551/141‑1 (MQ=255)                                                                                                     ttGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgccaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttttggtattgaaaataaaaaagggcacaaaagaggca                              <  2:39775‑M2/141‑106 (MQ=255)                                                                                                     ttGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTCTATGATATTTAGGAATGAGATGCTATTa                              >  2:101362/1‑141 (MQ=255)                                                                                                       gATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACg                            >  1:244293/1‑141 (MQ=255)                                                                                                        aTTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGAGGTTGCTGGGCGTGTTAATTTAAACAGGGATTTATATGATATTTAGGAATGAGATGCTATTACgg                           >  1:195032/1‑141 (MQ=255)                                                                                                           gCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATa                        <  2:237671/141‑1 (MQ=255)                                                                                                           gCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTAAGTAAAGTGATGTTGTTGGGCTTTTTAATTTAAACAGATATTTTTTGTATATTTATGAATGATATGTTATTCCTGATa                        >  2:54364/1‑141 (MQ=255)                                                                                                            cccTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATaa                       >  2:114568/1‑141 (MQ=255)                                                                                                                      tCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaatacaaataccctttaataacaacgattaaggggatatttttgtggtattgaaaataaaaaagggcacaaaaagggctgtatatgcaaactaacg             <  2:131704‑M2/141‑123 (MQ=255)                                                                                                                      tCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATcc             <  1:44172/141‑1 (MQ=255)                                                                                                                        cTTGATACTCTGGCTAATTATTCCTGCTAAGTAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGAGATTTTTAATTTACACAGGTATTTATATGAAATTTAGGTATTCAATACTATTACGGATAAATTaacagcata           >  2:131981/1‑134 (MQ=255)                                                                                                                              aaTCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGGTGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATatgca     >  1:104602/1‑141 (MQ=255)                                                                                                                                 ttGGCTAATTATGCCTGTGAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATatgcatgc  <  2:284542/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                      GTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGC  >  USA300TCH1516_ALE/909605‑909873

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.