New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 2085296 =15 (0.490)4 (0.150) 4/230 NT 19.3% intergenic (‑558/‑400) mapW2/USA300HOU_1944 cell surface protein MapW2/hypothetical protein
?CP000730 = 2128343 20 (0.730)intergenic (+57/+1062) int/USA300HOU_2011 bacteriophage integrase/possible leukocidin subunit

AAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGG  >  CP000730/2085159‑2085429
                                                                                                                                         |                                                                                                                                     
catccgtgtattctcatttggtagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGt                                                                                                                                     <  2:269632‑M1/3‑1 (MQ=255)
   ccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttagaaggtttctaTGTATc                                                                                                                                  <  1:297600‑M1/6‑1 (MQ=255)
      tgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCaa                                                                                                                               <  1:357613‑M1/9‑1 (MQ=255)
        tattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAAc                                                                                                                             >  1:149427‑M1/130‑140 (MQ=255)
        tattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAAc                                                                                                                             >  2:248277‑M1/130‑140 (MQ=255)
          acacTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTG                                                                                                                           <  1:157538‑M1/140‑1 (MQ=255)
            ctcatctgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaatttaagaaagtatgtaatttaggcacccactagggactccaaccccaataaatactgttgttacaaggattctaTgtgtccaacacggg                                                                                                                         <  2:36317‑M1/15‑7 (MQ=255)
            acTTGCATTAGCAAATTTNTTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGga                                                                                                                         <  1:306851/140‑1 (MQ=255)
              ttGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGaaga                                                                                                                       >  1:266634‑M1/1‑136 (MQ=255)
               tGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATATTACCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGAc                                                                                                                      <  1:280539/140‑1 (MQ=255)
                   gtaccaaatTTATTAGTAGTTGGTGTGCTTACTGACACTAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGgggcaata                                                                                                                  <  2:81047‑M1/136‑9 (MQ=255)
                          aTTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATaa                                                                                                           >  1:175144/1‑140 (MQ=255)
                                     gTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATc                                                                                                <  1:238607/140‑1 (MQ=255)
                                       aagaggacaaaaaaacaactaaagttttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCAt                                                                                              >  2:102845‑M1/99‑140 (MQ=255)
                                         gTGCACTTAGTGACAATAGAGCCAAACCTGAATCTACGAAACATGACACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCATTTTGTATCCAAACTGGAGACTTTTAACATAAAATTAATTATCATTc                                                                                            >  2:67586/1‑140 (MQ=255)
                                              cTTACTGACAATAGTGACAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGgggcaatataaacgcgctgatttaatcggacaatc                                                                                       <  2:44665‑M1/140‑36 (MQ=255)
                                               ttagggACAATCGTGCCAAAGGCTAATCTAAGAAAGATGAGACTGATGTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAg                                                                                      <  1:45989/135‑1 (MQ=255)
                                                  cTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGATTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCACAAACTaa                                                                                   >  2:293594/1‑140 (MQ=255)
                                                        aTAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGATAGTTAGTCATAACGTTTATATGTGATCGACCGTTTTGTATACAAACTGGgggcaatataaacgcgctgatttaatcggaaaaactacttgtatt                                                                             >  2:34939‑M1/1‑95 (MQ=255)
                                                                    ccGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAga                                                                 >  2:75944/1‑139 (MQ=255)
                                                                      aagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAACAAGTAAAACAGCATAATATcaagttt                                                               <  1:151492‑M1/73‑4 (MQ=255)
                                                                         tatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTtat                                                            >  2:207118‑M1/65‑140 (MQ=255)
                                                                            aagaaagaTGATACTGAGCTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTGTTATCATCGCATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAAc                                                         <  1:50614/140‑1 (MQ=255)
                                                                            aagaaagaTGATACAGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGTATAATATCAAGGCTTATAAc                                                         <  1:222921/140‑1 (MQ=255)
                                                                                  gatgatACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatc                                                   <  2:354666/140‑1 (MQ=255)
                                                                                     gatACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCACACTGGgggcaatataaacgcgcggatttaatcggacaatcttcttatattaaaaataatgatgtcgtaatattcaatga                                                >  2:310326‑M1/1‑66 (MQ=255)
                                                                                         cggatTTGTAGTTAGTTAGTCATAACGTTTATATTTTATCGACCGTGTTGTATCCAAACTGGgggcaatataaacgcgctgatttaatcggacaatcttcttatattaaaaataatgatgtcgtaatattcaatgaagca                                            <  1:118490‑M1/138‑79 (MQ=255)
                                                                                         ccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattatca                                            >  1:39191‑M1/49‑140 (MQ=255)
                                                                                         cTGATTTGAAGTTAGATAGTCATATAGTTTATCTGTTATCGACCGTTTTGAATCCAAACTGGAGACTTTTAACATAAAATTACTTATTATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatcattatca                                            <  1:206556/140‑1 (MQ=255)
                                                                                                  ttgtatttagtTATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACCGCATAATATCAAGGTTTATAACTGTATCATTATCAATAATACCt                                   <  1:216339/134‑1 (MQ=255)
                                                                                                                  cGTTTATATGTTATCTACCCTTTTGTATCCAAACTAGAGACTTTTAACATAAAATTACTTATCATTCCAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAtt                   <  2:215222/140‑1 (MQ=255)
                                                                                                                               tCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggacttttt      <  2:175144/140‑1 (MQ=255)
                                                                                                                                   ccGTTTTGTATCCAAACTGGgggcaatataaacgcgctgatttaatcggaccatgttcgaaaattaaaaataatgatgtcgtaatattcaatgaagcatttgataatggtgcatcagacaaattattaagtaatgtgaaa  <  1:350536‑M1/140‑121 (MQ=255)
                                                                                                                                         |                                                                                                                                     
AAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGG  >  CP000730/2085159‑2085429

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.