New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 2085296 =34 (1.300)12 (0.510) 11/252 1.0 30.2% coding (173/201 nt) hlb_1 Phospholipase C
?USA300TCH1516_ALE = 2128343 25 (1.060)coding (1/825 nt) hlb_2 Phospholipase C

CATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAA  >  USA300TCH1516_ALE/2128207‑2128483
                                                                                                                                        |                                                                                                                                            
cATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgta                                                                                                                                          >  1:73878‑M2/1‑137 (MQ=255)
 aTCGGTGTGTTATCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtat                                                                                                                                         >  2:291356‑M2/1‑136 (MQ=255)
 aTCCGTGTATTCTAATGTAATAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtat                                                                                                                                         >  2:32537‑M2/1‑136 (MQ=255)
  aacatgtatacACATTTGTTAGAAGAAAAATTTAATGAAGAAGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatc                                                                                                                                        >  2:41111‑M2/5‑135 (MQ=255)
    cGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTCtgtatcca                                                                                                                                      <  2:289802‑M2/141‑9 (MQ=255)
    cGTGTATTCTCATTTGTTAGAAGAAAAATGTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatcca                                                                                                                                      <  1:28360‑M2/141‑9 (MQ=255)
      tgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGCATATAAATAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaa                                                                                                                                    >  1:143004‑M2/1‑131 (MQ=255)
        tataataatttgttaGAAGAAAAATTTAATGAAGAAGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaact                                                                                                                                  >  2:71234‑M2/8‑129 (MQ=255)
          ttCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactgg                                                                                                                                <  2:223367‑M2/141‑15 (MQ=255)
           tctcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactgga                                                                                                                               >  1:214106‑M2/1‑126 (MQ=255)
             taaTTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTGAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTggggg                                                                                                                             <  1:32545/139‑1 (MQ=255)
                     tAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaac                                                                                                                     >  1:7902‑M2/1‑116 (MQ=255)
                      agaagaAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATaaa                                                                                                                    >  2:224576/1‑141 (MQ=255)
                      agaagaAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATGTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaaca                                                                                                                    >  2:115670‑M2/1‑115 (MQ=255)
                        aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCCTTAGGGACTCAACAAACAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAcg                                                                                                                  >  1:286505/1‑141 (MQ=255)
                        aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacata                                                                                                                  >  2:198029‑M2/1‑113 (MQ=255)
                             aaaTTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAGCGCGCTg                                                                                                             >  1:163466/1‑141 (MQ=255)
                             aaaTTAAATGAAGAAGAAAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTg                                                                                                             <  2:117764/141‑1 (MQ=255)
                             aaaTGTAAAGAAGAGGACAAAAAAACAACTAAAATTTAAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTg                                                                                                             <  2:244249/141‑1 (MQ=255)
                                       aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                   <  2:279241/141‑1 (MQ=255)
                                       aaGAGGAAAAAAAAACAACTAAAAGTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                   <  2:258191/141‑1 (MQ=255)
                                                aaaaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagta                                                                                          >  2:28360‑M2/1‑89 (MQ=255)
                                                  aaaaCAACGAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACAGGGGGCAATATAAACGCGCTGATTTAATCGGACAATcttctt                                                                                        >  2:266542/1‑141 (MQ=255)
                                                   aaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTta                                                                                       <  1:234146/141‑1 (MQ=255)
                                                    aacaacTAAAATTTGAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTtat                                                                                      <  1:14853/141‑1 (MQ=255)
                                                        acTAAAATTTTAGAAAGTCTGTAATTTAGGGACCCATTAGGGACTCCAAACCAAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTTGGGGCACTATAAACGACATGATTTAATCAGACAATCTACTCatatcc                                                                                  >  2:72256/1‑139 (MQ=255)
                                                            aaaTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTaaaaa                                                                              >  2:169274/1‑141 (MQ=255)
                                                             aaTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataata                                                                             >  1:302770‑M2/1‑76 (MQ=255)
                                                             aaTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaat                                                                             <  1:30527/141‑1 (MQ=255)
                                                              aTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatat                                                                            <  1:73357‑M2/141‑67 (MQ=255)
                                                                tttAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatca                                                                          <  1:163400‑M2/141‑69 (MQ=255)
                                                                   aGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAatgat                                                                       >  1:213840/1‑141 (MQ=255)
                                                                       aGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCAAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGAGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCg                                                                   >  2:301405/1‑141 (MQ=255)
                                                                          atatAAGTTAGGGAACAATTAGGGAATCAAAAACCAATAAATACTATTGTTATAAGGTTTTTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataa                                                                >  2:66769‑M2/1‑63 (MQ=255)
                                                                             tAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAatat                                                             >  2:239203/1‑141 (MQ=255)
                                                                                            ttAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTACCAATAATGAAGTCGTAATATTCAATGAAGCATTTg                                              <  1:224576/141‑1 (MQ=255)
                                                                                                        aaCCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaagagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataa                                  <  1:26580‑M2/141‑109 (MQ=255)
                                                                                                        aaCCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataa                                  <  1:105431‑M2/141‑109 (MQ=255)
                                                                                                           ccAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGATAATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAg                               >  2:263613/1‑141 (MQ=255)
                                                                                                                   taCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAatta                       <  1:223367/141‑1 (MQ=255)
                                                                                                                      tgttgtTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAAttatta                    >  1:13073/1‑141 (MQ=255)
                                                                                                                              aaaGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAAtgt            <  1:258895/140‑1 (MQ=255)
                                                                                                                                aGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggactttttag          >  2:96953‑M2/1‑9 (MQ=255)
                                                                                                                                aGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATAATAAAAATAACGAAAGCCGATTAGACTATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGa          >  1:286753/1‑141 (MQ=255)
                                                                                                                                      cTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAg    <  1:266542/141‑1 (MQ=255)
                                                                                                                                        aTGTATCCAAACTGGGGGCATTTGAAATGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGaa  >  2:186217/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                            
CATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAA  >  USA300TCH1516_ALE/2128207‑2128483

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.