New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 512620 =23 (1.130)21 (1.440)
+TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA
20/200 0.0 56.2% intergenic (+688/‑6075) recR/speA_2 Recombination protein RecR/Arginine decarboxylase
?USA300TCH1516_ALE 1998278 = NA (NA)intergenic (‑6/+3329) USA300TCH1516_01882/USA300TCH1516_01883 tRNA‑Val/tRNA‑Ala

ATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATTAACATTTAAGTCAATAACTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/512752‑512620
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAA  >  USA300TCH1516_ALE/1998278‑1998406
                                                                                                                                     ||||||||||||||||||||||||||||||||||||||||                                                                                                                                 
ATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTCTACATTTTATCAACATTTAATTCAATAACTTTTTTTATCTTG                                                                                                                                                                   >  2:189961/1‑141
        TGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTAAATGGTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACCTTTAAGTCAATAACTTTTTTTATCTTGTCCATTTT                                                                                                                                                           >  2:96651/1‑141
                            TTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATCTACAATTTTCTTACCGACAAGAATTACTCTGACAATTTATCAACATTTAATAAATTAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGA                                                                                                                                       >  1:210671/1‑141
                                   TTAACGTTGACATATTGTCATTCAGTTTTCAATGGTCATGTTTATTACCGACAAGAATTAATTATACCTTTTAGCCACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAA                                                                                                                                <  1:32988/141‑1
                                           GACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAATACTGCCTt                                                                                                                        >  2:201607/1‑140
                                                    gCATGCAGTTTTGAATGTTCAGTTTTCTGACCGTCAAGAATTAATTATACATTGTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCAGTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTC                                                                                                               <  2:149120/140‑1
                                                        TCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCGAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACT                                                                                                           <  1:42286/141‑1
                                                             TTTAAATGTTCATTTTTCATACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGCTCTACTCTAGC                                                                                                      <  2:194394/141‑1
                                                                    GTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATCACTTACTTTTTCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGT                                                                                               <  2:84344/141‑1
                                                                     TTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTA                                                                                              >  1:220694/1‑141
                                                                        ATTTTTCGTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGT                                                                                           <  2:102490/141‑1
                                                                          TTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTC                                                                                         >  1:235913/1‑141
                                                                             TCTTACCTACAAAAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTAATTAAAAAACTGCCTGGCAACGTTCTACCCTAGCGGAACGTAAGTTCGAC                                                                                      <  1:185982/141‑1
                                                                             TCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTTATTAAAAAACTGCCTGTCAACGTTCTACTCTAGCTGAACTTAAGTTCGAC                                                                                      >  2:221373/1‑141
                                                                                   CGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCAT                                                                                <  1:1772/141‑1
                                                                                             TAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAG                                                                      <  1:83162/141‑1
                                                                                                     CATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAA                                                              <  2:220694/141‑1
                                                                                                          TATAAAGATGTAAGTCAAGAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCT                                                         <  2:25062/141‑1
                                                                                                            tcAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGCACGTAAGTTCGACTACCATCGACGCTAGGGAGCTTAACTTCTGT                                                       >  1:213255/3‑141
                                                                                                              AACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACCACCATCGACGCTAAGGAGCTTAACTTCTGTGT                                                     <  2:210671/141‑1
                                                                                                               ACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGTCAACGTTCTACTCTAGCGGAACTTAAGTTCGACTACCATCGACGCTAACGAGCTTAACTTCTTTGTT                                                    >  2:54872/1‑141
                                                                                                                      AGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATG                                             >  1:25969/1‑141
                                                                                                                             AACTTTTTTTATCTTGTCCATTTTATTTGTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAG                                      <  2:146504/141‑1
                                                                                                                              ACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGG                                     >  1:85531/1‑141
                                                                                                                                       attTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTC                            <  1:189961/138‑1
                                                                                                                                                ATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATA                   >  1:88038/1‑141
                                                                                                                                                          TTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGAC         <  1:201607/141‑1
                                                                                                                                                                 AAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTATCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTCACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCGTGCTATAGTAACCAGACATATGAA  >  2:98929/1‑141
                                                                                                                                     ||||||||||||||||||||||||||||||||||||||||                                                                                                                                 
ATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATTAACATTTAAGTCAATAACTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/512752‑512620
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAA  >  USA300TCH1516_ALE/1998278‑1998406

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.