New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 895785 =18 (0.640)6 (0.250) 4/244 2.9 28.7% coding (806/822 nt) metQ_2 Methionine‑binding lipoprotein MetQ
?USA300TCH1516_ALE = 909740 14 (0.570)intergenic (‑663/‑371) USA300HOU_RS04500/csbD_1 hypothetical protein/Stress response protein CsbD

TGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAA  >  USA300TCH1516_ALE/895648‑895922
                                                                                                                                         |                                                                                                                                         
tGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGCTGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTACAGTTa                                                                                                                                         >  2:294769/1‑140 (MQ=255)
  ttttcaagggcaaaagaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaattatt                                                                                                                                       >  1:141633‑M1/136‑140 (MQ=255)
  cGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTAAAGACTTCATTAATGAAAAATACAATGGTGCAattatt                                                                                                                                       >  2:242640/1‑140 (MQ=255)
    ttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTcc                                                                                                                                     <  1:214956‑M1/7‑1 (MQ=255)
     tcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTc                                                                                                                                      <  1:198268‑M1/6‑1 (MQ=255)
     tcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTc                                                                                                                                      >  2:198268‑M1/133‑138 (MQ=255)
       aagggcaaaaaaatggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGc                                                                                                                                  >  1:69718‑M1/131‑140 (MQ=255)
       aagggcaaaaaaagggaataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGc                                                                                                                                  >  1:186526‑M1/131‑140 (MQ=255)
            tCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAaat                                                                                                                             >  1:225834/1‑140 (MQ=255)
                    cataattAATTGCGGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCaa                                                                                                                     <  2:95618/135‑1 (MQ=255)
                           aaTTGCTGTTAAAGAAGTACATCAAGATGATAAGAAAATTAAAGACTTGCTGGAAGTATTACAATCTAAAGATATTTAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaata                                                                                                              <  2:197129/140‑1 (MQ=255)
                           aaTTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTATTGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaata                                                                                                              <  1:189046/140‑1 (MQ=255)
                              tGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATaaaa                                                                                                           >  1:256036/1‑140 (MQ=255)
                                      aagaagGACATCGAGATGAAAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCtt                                                                                                   <  2:90065/140‑1 (MQ=255)
                                             agggtatgaataataaattatcttaaaaattttataaatgcatatataacaatgttttgattgcacttgaacttccttgataatctgactaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATCCCATTTAAAaac                                                                                            <  2:20869‑M1/48‑1 (MQ=255)
                                             aCATCAAGATGATAAGAAAATCAAAGCACTAATTGAAGTATTACAATCCAAAGATATTAAAGACTTCATTAAGGAAAAATACAATGGTGCAGTTATTCCAGCTAAATAATACCAATTAAATAAAAATACCCTTTAATaac                                                                                            <  2:22812/140‑1 (MQ=255)
                                               aTCAAGATGATAAGAAAATCAAAGCCTTGGATGAAGGATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCATTAATaacaa                                                                                          >  2:149911/1‑140 (MQ=255)
                                                                   aaaGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAACGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATCAAGGGGTTATTTTtg                                                                      >  2:190436/1‑140 (MQ=255)
                                                                             ttGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTGTTGGGTTATTGag                                                            >  1:44557/1‑139 (MQ=255)
                                                                              tGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaaa                                                           <  1:224426/140‑1 (MQ=255)
                                                                                  atgtatatataacaatgttttgattgcccttgaacttcctttataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATaa                                                       >  2:166211‑M1/56‑140 (MQ=255)
                                                                                  atgcatatataacaatgttttgattgcccttgaacttactggataatctggctaaTTATTCCTGCTAAATAATAACAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATaa                                                       >  2:1105‑M1/56‑140 (MQ=255)
                                                                                                     ttCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGc                                    <  2:256036/140‑1 (MQ=255)
                                                                                                      tCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGACa                                   >  1:55870/1‑140 (MQ=255)
                                                                                                        aaGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGTAAATAAAAAAAATCACAAAATGAGCAGt                                 >  1:204882/1‑140 (MQ=255)
                                                                                                          tgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTAATTTTTGTGGTATTGAAAATAAAAAAGGGCACACAAGGGGCAGtat                               <  1:219493‑M1/109‑1 (MQ=255)
                                                                                                                                     gCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACaaaa    >  1:10974/1‑140 (MQ=255)
                                                                                                                                     gCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGAGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACaaaa    >  1:311602/1‑140 (MQ=255)
                                                                                                                                       aaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAATAAGGTCACAAAAGGTGTTGTTTATGCAAATTATCGAATTTTAAACaaaaaa  <  1:106585‑M1/138‑1 (MQ=255)
                                                                                                                                       aaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACaaaaaa  <  1:320475‑M1/138‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                         
TGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAA  >  USA300TCH1516_ALE/895648‑895922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.