New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 2085296 =18 (0.650)21 (0.840) 17/252 0.4 53.7% coding (173/201 nt) hlb_1 Phospholipase C
?USA300TCH1516_ALE = 2128343 20 (0.800)coding (1/825 nt) hlb_2 Phospholipase C

AAAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACTTTA  >  USA300TCH1516_ALE/2085156‑2085435
                                                                                                                                            |                                                                                                                                           
ctacatccgtgtattctcatttgttagaagaaaaatttaatgaagagtacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctat                                                                                                                                             <  2:165852‑M1/1‑1 (MQ=255)
  acatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGt                                                                                                                                           <  1:111555‑M1/3‑1 (MQ=255)
  acatccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGt                                                                                                                                           <  1:317258‑M1/3‑1 (MQ=255)
   catccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaattatgtaatttagagacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTa                                                                                                                                          <  2:60117‑M1/4‑1 (MQ=255)
   catccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTa                                                                                                                                          <  2:165307‑M1/4‑1 (MQ=255)
    atccgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactggtgttacaaggtttctaTGTAt                                                                                                                                         >  1:37717‑M1/137‑141 (MQ=255)
    atccgtgtattataaattgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTAt                                                                                                                                         >  2:124759‑M1/137‑141 (MQ=255)
      ccgtgtattctcatttgttagaagacaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATcc                                                                                                                                       >  1:201663‑M1/135‑141 (MQ=255)
       cgtgtattctcatttgttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCa                                                                                                                                      <  2:2503‑M1/8‑1 (MQ=255)
        atagagtctaatttgtaagaagaaaaatttaatgaagagaacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCaa                                                                                                                                     >  2:187823‑M1/133‑141 (MQ=255)
         tGCAATACTTGCATTAGAAAATTTATTATTAGTTGTTGCACTTACTGACAATATTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTGTATCCAAAc                                                                                                                                   <  2:200484/141‑1 (MQ=255)
             agctcatttataagaagaaaaatttaatgaagagaaaaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTgg                                                                                                                                >  2:299516‑M1/128‑141 (MQ=255)
                      gttagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactacaaacataggaaatactgatgttacaagggttctaTGTATCCAAACTGGAGACTTTTa                                                                                                                       <  1:150555‑M1/23‑1 (MQ=255)
                        tagaagaaaaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAAc                                                                                                                     <  2:233722‑M1/25‑1 (MQ=255)
                         agaagaaaaatgtaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACa                                                                                                                    >  2:241142‑M1/116‑141 (MQ=255)
                               agaaattaatgaagcggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAAt                                                                                                              >  1:316628‑M1/110‑141 (MQ=255)
                                aaatttaatgaagaggacaaaaaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgctacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAAtt                                                                                                             >  2:216507‑M1/109‑141 (MQ=255)
                                 attagtaGTTGGTGCACTTACTGACAATAGTGACAAACTCGAATCTAAGAAAGATGTGACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTa                                                                                                            <  2:130610/141‑1 (MQ=255)
                                              gCACTTACTGACAATAGTGCCAAAGGCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCaaa                                                                                               <  1:210890/141‑1 (MQ=255)
                                                acaaaaaaacaactaaaattttagaaagtatgtaatttagggaccaattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAAATGGAGACTTTTAACATAAAATTTCTTATCAttcaataa                                                                                             <  2:151848‑M1/49‑4 (MQ=255)
                                                 cTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAg                                                                                            <  1:90129/141‑1 (MQ=255)
                                                     aaaacaactaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTaaa                                                                                        <  1:100898‑M1/54‑1 (MQ=255)
                                                       gACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAAc                                                                                      <  1:209158/141‑1 (MQ=255)
                                                           actaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAaacaaca                                                                                  <  2:219701‑M1/60‑4 (MQ=255)
                                                           actaaaattttagaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTAAAAAAGTAAAACAGCa                                                                                  <  2:305398‑M1/60‑1 (MQ=255)
                                                            tAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCat                                                                                 <  1:263127/141‑1 (MQ=255)
                                                                aattttagaaagtatgtaatttagggacccattagggactccaaacccaataaattctgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCataata                                                                             >  2:3126‑M1/77‑141 (MQ=255)
                                                                aattttagaaagtatgtaacttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCataata                                                                             >  1:96667‑M1/77‑141 (MQ=255)
                                                                      agaaagtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAgg                                                                       <  2:222430‑M1/71‑1 (MQ=255)
                                                                          agtatgtaatttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTta                                                                   >  2:188543‑M1/67‑141 (MQ=255)
                                                                           aTCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTtat                                                                  >  1:84276/1‑141 (MQ=255)
                                                                                    ttagggacccattagggactccaaacccaataaatactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTttatc                                                         >  2:25845‑M1/57‑141 (MQ=255)
                                                                                            cTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCaa                                                 >  2:251887/1‑141 (MQ=255)
                                                                                             tGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTGATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCaat                                                <  2:54411/141‑1 (MQ=255)
                                                                                                         agttagtCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTAATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACATCatat                                    >  2:29777/1‑141 (MQ=255)
                                                                                                             agtCATAACGTTTATATGTTATCGACCGTTTTGTATCAAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACATCATataaaa                                >  1:118219/1‑141 (MQ=255)
                                                                                                                     atactgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAACCAGAGTATTATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttt                        >  1:204515‑M1/24‑141 (MQ=255)
                                                                                                                     atactgttgttacaaggtttccaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttt                        >  2:79604‑M1/24‑141 (MQ=255)
                                                                                                                        ctgttgttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAattttaa                     <  2:109801‑M1/121‑2 (MQ=255)
                                                                                                                             tGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggact                <  1:199328/141‑1 (MQ=255)
                                                                                                                             gttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggact                <  2:203183‑M1/126‑1 (MQ=255)
                                                                                                                             gttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggact                <  1:14851‑M1/126‑1 (MQ=255)
                                                                                                                              ttacaaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAACAttttagggactt               <  2:95970‑M1/127‑1 (MQ=255)
                                                                                                                                  aaggtttctaTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggacttttta           >  1:159311‑M1/11‑141 (MQ=255)
                                                                                                                                    gACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttttagg         <  1:11481/141‑1 (MQ=255)
                                                                                                                                    gACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttttagg         >  1:274430/1‑141 (MQ=255)
                                                                                                                                       cGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAAttttagggactttttagggac      <  2:265314/141‑1 (MQ=255)
                                                                                                                                         ttttGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATtttagggactttttagggactt    >  1:138086/1‑141 (MQ=255)
                                                                                                                                         ttttGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATtttagggactttttagggactt    <  1:4454/141‑1 (MQ=255)
                                                                                                                                           ttGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATATTAGGGACACTTTAGGTACttta  >  2:199082/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                           
AAAAAAAGTTGCAACACTTGCATTAGCAAATTTATTATTAGTTGGTGCACTTACTGACAATAGTGCCAAAGCCGAATCTAAGAAAGATGATACTGATTTGAAGTTAGTTAGTCATAACGTTTATATGTTATCGACCGTTTTGTATCCAAACTGGAGACTTTTAACATAAAATTACTTATCATTCAAAAAGTAAAACAGCATAATATCAAGGTTTATAACTTTATCATTATCAATAATACCTCATATAAAATAAAATTTTAGGGACTTTTTAGGGACTTTA  >  USA300TCH1516_ALE/2085156‑2085435

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.