New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 1456948 =174 (0.950)17 (0.100)
+GTTTT		 4/244 NT 8.7% intergenic (‑62/‑182) USA300HOU_RS07230/USA300HOU_RS07235 hypothetical protein/hypothetical protein
?USA300TCH1516_ALE = 1918540 199 (1.090)intergenic (‑258/+240) USA300HOU_RS07235/USA300HOU_RS09510 hypothetical protein/hypothetical protein

CAAAAGCAGTAAACCTAAAGTGTCGTAAGGGTTTACTGCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1456990‑1456948
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTTAATGTC  <  USA300TCH1516_ALE/1918540‑1918401
                                           |||||                                                                                                                                            
CAAAAGCAGTAAACCTAAAGTGTCGTAAGGGTTTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATT                                                 >  3:291820/1‑141
 AAAAGCAGTAAACCTAAAGTGTCGTAAGGGTTTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTG                                                >  2:111686/1‑141
        GTAAACCTAAAGTGTCGTAAGGGTTTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCC                                         >  2:679663/1‑141
               TAAAGTGTCGTAAGGGTTTACTGCTTTTGTTTTTTTTTTTATTACAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAA                                  >  4:53702/1‑141
               TAAAGTGTCGTAAGGGTTTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAA                                  >  2:935270/1‑141
                          ttatGTTTACTGCTTTTGTTTTTTGTAAACAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACAC                       <  4:334635/137‑1
                             GGTTTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAG                    >  1:1240608/1‑141
                              GTTTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGG                   >  1:143189/1‑141
                              GTTTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGG                   >  1:1126067/1‑141
                               TTTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACA                                                                                  >  1:1557829/1‑77
                               TTTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACA                                                                                  <  2:1557829/77‑1
                                TTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTGGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAG                 >  1:1303809/1‑141
                                TTACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAG                 >  1:483903/1‑141
                                  ACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGatgat               >  3:617835/1‑136
                                  ACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGAT               >  2:565975/1‑141
                                  ACTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGAT               <  3:308754/141‑1
                                   CTGCTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCATCCAAAATAATCAACACGAGGAGATG              <  1:1547260/141‑1
                                      CTTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTA           <  1:128738/141‑1
                                       TTTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTAT          >  1:1018490/1‑141
                                        TTTGTTTTTTGTAAAAAGAAACCCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATT         <  3:229104/141‑1
                                        TTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATT         <  2:392389/141‑1
                                        TTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATT         >  1:1595257/1‑141
                                        TTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATT         <  2:790854/141‑1
                                        TTTGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATT         >  2:831818/1‑141
                                         TTGTATTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTT        <  4:639486/141‑1
                                          TGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTTA       <  2:1535937/141‑1
                                          TGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTTA       <  4:322477/141‑1
                                          TGTTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTTA       <  4:55158/141‑1
                                            TTTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTTAAT     >  1:1389555/1‑141
                                            TTTTTGGTAAAAAGAATACCATACGCTATGCGTATGGTTCAGAAAGGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTTAAT     <  1:1005033/141‑1
                                             TTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAA                                                     <  2:1188766/92‑1
                                             TTTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAA                                                     >  1:1188766/1‑92
                                              TTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTTAATGT   <  2:1124620/141‑1
                                              TTTTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTTAATGT   <  2:1085301/141‑1
                                               TTTTTAAAAATTAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACAATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACTAGGAGAGTCTATTTAATTTC  >  4:368804/1‑141
                                               TTTGTAAAAAGAAAACCATACGCTCTGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAAAACGAGGAGATGCTATTTAATGTC  <  1:711096/141‑1
                                           |||||                                                                                                                                            
CAAAAGCAGTAAACCTAAAGTGTCGTAAGGGTTTACTGCTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1456990‑1456948
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TTGTAAAAAGAAAACCATACGCTATGCGTATGGTTCAGAAAAGGTTCTACCATTGTCACAAAAAATGCATCTCTACGTGCTAGAATAAATATTGGTCAGCCAACCAAAATAATCAACACGAGGAGATGCTATTTAATGTC  <  USA300TCH1516_ALE/1918540‑1918401

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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.