New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 1533866 =173 (0.950)9 (0.050) 9/232 NT 5.7% coding (219/588 nt) USA300HOU_RS07480 hypothetical protein
?USA300TCH1516_ALE 1533900 = 138 (0.830)coding (185/588 nt) USA300HOU_RS07480 hypothetical protein

ATATCGATTTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGCAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1534016‑1533866
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttctgcaattTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTCAATAAA  >  USA300TCH1516_ALE/1533900‑1534039
                                                                                                                                                                                                                                                                                                   
ATATCGATTTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGC                                                                                                                                                        <  3:395988/141‑1
   ttttTTTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTC                                                                                                                                                     >  2:609303/5‑141
    CGATTTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCT                                                                                                                                                    <  1:1505612/141‑1
    CGATTTAAGTCGCGTATTGCAGCTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCT                                                                                                                                                    >  1:346348/1‑141
      ATTTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGTGGCGAAATTGGCAAACAGTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGC                                                                                                                                                  <  4:607531/141‑1
      ATTTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGTAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGC                                                                                                                                                  <  2:276200/141‑1
      ATTTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGC                                                                                                                                                  <  1:1520298/141‑1
      ATTTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAAGTAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGC                                                                                                                                                  <  3:509321/141‑1
        TTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGCAA                                                                                                                                                <  1:1156524/141‑1
           AGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTATGCAATac                                                                                                                                             >  2:895761/1‑139
                        AGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGCAA                                                                                                                                                <  4:503358/125‑1
                        AGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGCAA                                                                                                                                                >  3:503358/1‑125
                                       CTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGACGTCACGCTTCTGC                                                                                                                                                  >  1:1263090/1‑108
                                       CTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGC                                                                                                                                                  <  2:1263090/108‑1
                                         ATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGCGTGACTTCCCACTTCTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTAT                                                                                                               <  2:447119/141‑1
                                                                      AACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGCGTGACTTCCCACTTCTGCAATTTCTAATGTTTCATGATGA                                                                                                                            >  1:951776/1‑99
                                                                      AACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGCGTGACTTCCCACTTCTGCAATTTCTAATGTTTCATGATGA                                                                                                                            <  2:951776/99‑1
                                                                                                                        TGCAGAAGTGGGAAGTCACGCTTCTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAA                                >  1:1466294/1‑141
                                                                                                                               GTGGGAAGTCACGCTTCTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATAT                         >  2:960562/1‑141
                                                                                                                                TGGGGAGTCACGCTTCTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATT                        >  2:320456/1‑141
                                                                                                                                 GGGAAGTCACGCTTCTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTG                       >  2:79689/1‑141
                                                                                                                                  GGAAGTCACGCTTCTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCGCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGA                      >  3:187219/1‑141
                                                                                                                                    AAGTCACGCTTCTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAAAACGCGACTTAAATCGATATTGAAA                    >  3:507660/1‑141
                                                                                                                                             TTCTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATA           >  1:1129601/1‑141
                                                                                                                                               CTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAACAAGTAAATATT         >  1:809840/1‑141
                                                                                                                                               CTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATT         >  2:78859/1‑141
                                                                                                                                               CTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATT         >  2:1124103/1‑141
                                                                                                                                               CTGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATT         >  3:137850/1‑141
                                                                                                                                                TGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTC        >  1:588458/1‑141
                                                                                                                                                TGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTC        >  1:1414222/1‑141
                                                                                                                                                TGCAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTC        <  1:79689/141‑1
                                                                                                                                                  CAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTCAA      <  4:648692/141‑1
                                                                                                                                                  CAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTCAA      <  1:284911/141‑1
                                                                                                                                                  CAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTCAA      <  1:6980/141‑1
                                                                                                                                                  CAATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTCAA      >  2:1027205/1‑141
                                                                                                                                                   AATTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTCAAT     <  1:1629226/141‑1
                                                                                                                                                     TTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTCAATAA   >  1:1614231/1‑141
                                                                                                                                                     TTTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTCAATAA   <  1:347637/141‑1
                                                                                                                                                      TTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAACTATTCAATAAA  >  2:946704/1‑141
                                                                                                                                                                                                                                                                                                   
ATATCGATTTAAGTCGCGTATTGCAGTTTGGGTGCTTAACTATATAAAAGTGAATGAGGCGAAATTGGCAAACATTCATTTTGTAGATACAAAAATTAATCATCATGAAACATTAGAAATTGCAGAAGTGGGAAGTCACGCTTCTGCAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1534016‑1533866
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttctgcaattTCTAATGTTTCATGATGATTAATTTTTGTATCTACAAAATGAATGTTTGCCAATTTCGCCTCATTCACTTTTATATAGTTAAGCACCCAAACTGCAATACGCGACTTAAATCGATATTGAAAAAGTAAATATTCAATAAA  >  USA300TCH1516_ALE/1533900‑1534039

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.