New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 1026972 =183 (1.000)9 (0.050) 7/242 NT 5.1% intergenic (+13/‑221) USA300HOU_RS05060/USA300HOU_RS05065 hypothetical protein/Serine protease HtrA‑like protein
?USA300TCH1516_ALE 1027002 = 162 (0.930)intergenic (+43/‑191) USA300HOU_RS05060/USA300HOU_RS05065 hypothetical protein/Serine protease HtrA‑like protein

ATTTCTATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAACCTTAAACTAAATTAAGATTGTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1027117‑1026972
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttgtccTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAAATTAG  >  USA300TCH1516_ALE/1027002‑1027141
                                                                                                                                                                                                                                                                                              
ATTTCTATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAACCTTAAACTAAATTAAGAT                                                                                                                                                   <  2:3567/141‑1
 TTTCTATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAACCTTAAACTAAATTAAGATT                                                                                                                                                  <  3:656815/141‑1
 TTTCTATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTAAAAAAAATAAAAAAGGACAACCTTAAACTAAATTAAGATT                                                                                                                                                  <  2:1054110/141‑1
  TTCTATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAACCTTAAACTAAATTAAGATTG                                                                                                                                                 <  4:301639/141‑1
  TTCTATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAACCTTAAACTAAATTAAGATTG                                                                                                                                                 <  2:4868/141‑1
   TCTATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAACCTTAAACTAAATTAAGATTGT                                                                                                                                                >  1:55678/1‑141
   TCTATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAACCTTAAACTAAATTAAGATTGT                                                                                                                                                <  2:1612949/141‑1
     TATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAACCTTAAACTAAATTAAGATTGTCC                                                                                                                                              <  3:102527/141‑1
                               GCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAATCTTAATTTAGTTTAAGGTTGTCCTTTTTCATTTAATTGAGTGATTTATG                                                                                                                    <  1:338732/141‑1
                                          TAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAATCTTAATTTAGTTTAAGGTTGTCCTTTTTCATTTAAT                                                                                                                                 <  4:374226/117‑1
                                          TAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAATCTTAATTTAGTTTAAGGTTGTCCTTTTTCATTTAAT                                                                                                                                 >  3:374226/1‑117
                                                                                                                     GACAACCTTAAACTAAATTAAGATTGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAG                              >  2:1114246/1‑141
                                                                                                                      ACAACCTTAAACTAAATTAAGATTGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGA                             >  2:1531489/1‑141
                                                                                                                      ACAACCTTAAACTAAATTAAGATTGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGA                             >  2:152103/1‑141
                                                                                                                       CAACCTTAAACTAAATTAAGATTGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAA                            >  1:1105019/1‑141
                                                                                                                       CAACCTTAAACTAAATTAAGATTGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAA                            >  1:1436318/1‑141
                                                                                                                          CCTTAAACTAAATTAAGATTGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATT                         >  1:76642/1‑141
                                                                                                                                            TTGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAA       <  2:1581238/141‑1
                                                                                                                                            TTGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAA       <  2:1581611/141‑1
                                                                                                                                             TGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAAA      <  1:856799/141‑1
                                                                                                                                             TGTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAAA      <  1:856782/141‑1
                                                                                                                                              GTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTTTTTATTATTTATATAGATTTTAAAGCACAT     >  2:1292149/1‑141
                                                                                                                                              GTCCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAAAT     >  2:541755/1‑141
                                                                                                                                                CCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAAATTA   <  2:214282/141‑1
                                                                                                                                                CCTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAAATTA   <  2:1483392/141‑1
                                                                                                                                                 CTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAAATTAG  <  2:1524963/141‑1
                                                                                                                                                                                                                                                                                              
ATTTCTATTGAAAAAATGCTAAATATAAAAGGCACATTTTCTTAATACTATATCGCATCTTTTGATTCACATTCTTCAAAATCCATTTTTCATAAATCACTCAATTAAATGAAAAAGGACAACCTTAAACTAAATTAAGATTGTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1027117‑1026972
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttgtccTTTTTCATTTAATTGAGTGATTTATGAAAAATGGATTTTGAAGAATGTGAATCAAAAGATGCGATATAGTATTAAGAAAATGTGCCTTTTATATTTAGCATTTTTTCAATAGAAATTATATAGATTTTAAAGCAAATTAG  >  USA300TCH1516_ALE/1027002‑1027141

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