New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	68659 =	104 (0.470)	3 (0.020)	3/210	NT	3.1%	coding (775/852 nt)	USA300TCH1516_00061	hypothetical protein
	?	USA300TCH1516_ALE	= 68655	97 (0.510)					coding (771/852 nt)	USA300TCH1516_00061	hypothetical protein
Rejected: Frequency below/above cutoff threshold.

TATAAACAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/68807‑68659 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attattattattattattGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  <  USA300TCH1516_ALE/68655‑68523                                                                                                                                                                                                                                                                                            TATAAACAAAAGAGCCTATAATCCTAGGGCACTGAACACTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAAGGGATAAGTAGCATAGTTATTGTTGAATTCGATT                                                                                                                                                      >  2:1450044/1‑134  ATAAACTTACGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGTAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTA                                                                                                                                                     <  1:381407/134‑1   TAAACAAAAGAGCGTATAATGCTAGGGCACTGAACCGTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTAT                                                                                                                                                    <  2:921344/134‑1    AAACAAAATAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATT                                                                                                                                                   <  2:1711132/134‑1     AACAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTA                                                                                                                                                  >  2:1655246/1‑134     AACAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAAAAACATGATATAGGCTATTAATTATCTGTATTATACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTA                                                                                                                                                  >  1:1306767/1‑134       CAAAAGAGCCTATAATCCTAGGGCATTGAACCCTTAAAACGGGAACTTAATAAATACATTATGTTCTATGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATT                                                                                                                                                <  1:2240887/134‑1       CAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAATAGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGACTTGTTTGTGTTGAATTCGATTATTATg                                                                                                                                                <  2:1319643/134‑2       CAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTATTTATTGAATTCGATTATTATT                                                                                                                                                >  2:2617379/1‑134        AAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTA                                                                                                                                               <  1:20046/134‑1         AAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATTTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTAT                                                                                                                                              <  1:2485248/134‑1          AAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGTAACTTAATAAAAACATCATGTTCTATGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATT                                                                                                                                             <  1:992274/134‑1           AGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTA                                                                                                                                            >  1:2499264/1‑134             AGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGGATTCGATTATTATTATTATT                                                                                                                                          <  2:1867033/134‑1             AGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGCGCATACGTAGCCTCGCTTTTGTCGAATTCGCTTATTATTATTATT                                                                                                                                          >  2:146342/1‑134              GCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTCTTAATTCTCTGTATTTTACAGGGGATCTGTTGCCTGGTTTTTGTTGCATTCTATTATTACTATTATTA                                                                                                                                         >  1:846447/1‑134              GCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTA                                                                                                                                         <  1:2144077/134‑1              GCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTA                                                                                                                                         >  2:2840111/1‑134              GCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTATTTGTTGAATTCGATTATTATTATTATTA                                                                                                                                         >  2:1216062/1‑134              GCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGCCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTA                                                                                                                                         >  2:579870/1‑134               CCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTAT                                                                                                                                        <  2:1602067/134‑1               CCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTAT                                                                                                                                        <  2:1260213/134‑1               CCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAAAAGACTCGAAAATGTTGAATTCGATTATTATTATTATTAT                                                                                                                                        >  1:2702107/1‑134               CCTATAATCCTAGGGCACTGAACCCTTAAAACCGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGAGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTAT                                                                                                                                        >  2:2554874/1‑134                   TAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATTGTT                                                                                                                                    <  1:720243/134‑1                                    ACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATTGTTTTTAATGTACTTTTCGA                                                                                                                   >  1:2575614/1‑134                                                                                  AATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATTGTTTTTAATATACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAATCTCATTATTGAT                                                                     >  1:1944840/1‑134                                                                                                               GCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTAAAAAATAATTAGAGTAATTAAACTCATTATTGATGTAAAAAGTTTCAGAATTTAACGAAGAAT                                        >  1:433169/1‑134                                                                                                                                    acaATTATTATTATTTTTTTTTTTAATGTTCTTTTCGACAATATCTATTATAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGT                   <  1:2075877/131‑1                                                                                                                                    ATTATTATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATTTTATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGT                   <  1:2783623/134‑1                                                                                                                                         TATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCTTTATTGTTGTAAAAAGTTTCAGAATTTAACGAGGAATGGAAACTTTCAATAAGGGCGTTATCG              >  1:1042213/1‑134                                                                                                                                          ATTATTATTATTGTTTTTAATGTACTTTTCGAGAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGG             >  2:2555216/1‑134                                                                                                                                          ATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGG             >  1:2767632/1‑134                                                                                                                                          ATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGG             >  1:551812/1‑134                                                                                                                                           TTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGC            <  1:191661/134‑1                                                                                                                                           TTATTATTATGGTTTGTAAGGTACTTTTGGACAATATCTATTACAATGTGATTAGAGTGATTATGCTCATTATTGCTGTAAAGAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGC            <  2:2174149/134‑1                                                                                                                                            TATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCA           <  1:1387931/134‑1                                                                                                                                              TTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAATCTCATTATTTATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGCAGTTATCGGgcgg         >  2:1863718/1‑130                                                                                                                                              TTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGG         >  1:1551288/1‑134                                                                                                                                                ATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTG       >  2:1088743/1‑134                                                                                                                                                 TTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGT      <  2:1746765/134‑1                                                                                                                                                   ATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTC    >  1:1019889/1‑134                                                                                                                                                   ATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTC    >  1:2547841/1‑134                                                                                                                                                   ATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAACGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTC    >  1:1901882/1‑134                                                                                                                                                    TTGTTTTTAATGTACTTTTCTACTATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCC   <  1:848778/134‑1                                                                                                                                                    TTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAGACTTTCTATCGGGGCGTTATCGGCAGGTGTTCC   <  2:814303/134‑1                                                                                                                                                     TGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTTTTTATTGTTATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  <  1:2713941/134‑1                                                                                                                                                     TGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTTATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  >  1:805328/1‑134                                                                                                                                                     TGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  <  1:579870/134‑1                                                                                                                                                                                                                                                                                            TATAAACAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/68807‑68659 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attattattattattattGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  <  USA300TCH1516_ALE/68655‑68523

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.