New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 754401	164 (0.810)	22 (0.120)	12/146	NT	12.6%	coding (379/459 nt)	USA300HOU_RS03685	hypothetical protein
	?	USA300TCH1516_ALE	= 754417	155 (0.830)					coding (363/459 nt)	USA300HOU_RS03685	hypothetical protein

CGATTCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/754307‑754401 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaggtggTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGCT  <  USA300TCH1516_ALE/754417‑754328                                                                                                                                                                                           CGATTCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGCTCTTGCTTTGTAAAAG                                                                                                >  2:3790602/1‑91 CGATTCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAG                                                                                                >  1:2886993/1‑91 CGATTCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAG                                                                                                >  1:2171979/1‑91 CGATTCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTCATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAG                                                                                                >  1:3536587/1‑91  GATTCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGCCTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAACAGG                                                                                               >  2:537002/1‑91  GATTCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGG                                                                                               <  2:33554/91‑1     TCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGG                                                                                            >  1:1086076/1‑91     TCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGG                                                                                            >  2:1020724/1‑91     TCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGG                                                                                            >  2:2200720/1‑91     TCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGG                                                                                            >  2:351476/1‑91     TCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGG                                                                                            >  1:1085997/1‑91                TAATCCAGCTCCTTAATTCGCTGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTGAAAGGTGGTCGCCACAAAG                                                                                 <  2:1791463/91‑1                 AATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGG                                                                                <  2:334751/91‑1                  ATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGT                                                                               <  2:2899780/91‑1                   TCCAGCTCCTTAATTCTATGAATGACTTTTAATAGTGATTGTTCGAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTC                                                                              <  1:3143550/91‑1                    CCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCC                                                                             <  2:2611296/91‑1                     CAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCC                                                                            <  1:1835460/91‑1                      AGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCC                                                                           <  2:262397/91‑1                      AGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCC                                                                           <  2:2308490/91‑1                      AGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCC                                                                           <  2:429959/91‑1                      AGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCC                                                                           <  1:1150307/91‑1                      AGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCC                                                                           <  1:3604248/91‑1                      AGCTCCTGAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAGGGTCCCC                                                                           <  2:81682/91‑1                        gTCCTTAATTCGATGAATGGCTTTTAATGGTGATTGTTCAAACACTTTTTCATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCA                                                                         <  2:1580926/90‑1                        CTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCA                                                                         <  1:1367606/91‑1                         TCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCAC                                                                        <  1:1547773/91‑1                          CCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCACC                                                                       <  2:3277355/91‑1                          CCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCACC                                                                       <  2:1463721/91‑1                          CCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCACC                                                                       <  1:2119153/91‑1                          CCTTAAGTCGATGAATGACTTTTAATAGTGCTTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCACC                                                                       <  2:558542/91‑1                            TTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCACCTT                                                                     <  1:2055787/91‑1                            TTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCACCTT                                                                     <  1:2056136/91‑1                                     TGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGC                                                            <  1:2454815/91‑1                                                                                         AAGGTGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAA        <  2:109683/91‑1                                                                                         AAGGTGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAA        <  2:109906/91‑1                                                                                          AGGTGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAG       >  1:2618726/1‑91                                                                                          AGGTGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAG       >  1:2618204/1‑91                                                                                          AGGTGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAG       <  1:109301/91‑1                                                                                           GGTGGTCGCCACAAAGGTCCCCCACCTTCTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGG      >  2:2035741/1‑91                                                                                            GTGGTCGCCACAAATGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGA     <  2:3573916/91‑1                                                                                            GTGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGA     <  2:3573959/91‑1                                                                                            GTGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGA     >  1:1560389/1‑91                                                                                            GTGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGA     >  2:3479760/1‑91                                                                                            GTGGTCGACACAAAGGTCCCCCACCTTTTAAAAAAAAAAAAAAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGA     <  2:1041149/91‑1                                                                                             TGGTCGCCACAAAGGTCCCCCACCTTTTACCAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAG    >  2:1467138/1‑91                                                                                             TGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAG    >  1:3483349/1‑91                                                                                             TGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAG    >  2:3727521/1‑91                                                                                             TGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAG    >  2:794712/1‑91                                                                                             TGGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAG    >  1:3767361/1‑91                                                                                              GGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGC   >  1:1739624/1‑91                                                                                              GGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGC   <  2:3315336/91‑1                                                                                              GGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGC   <  2:2755403/91‑1                                                                                              GGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGC   >  1:1432965/1‑91                                                                                              GGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGC   <  1:3215311/91‑1                                                                                              GGTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGC   <  1:3215353/91‑1                                                                                              GGTCGCCACAAAAGTCCCCCACCTTTTACAAAACAAGAACAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGC   <  2:2700806/91‑1                                                                                               GTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACCATCACTATTAAAAGTCATTCATCGAATTAAGGAGCa  >  2:3917959/1‑90                                                                                               GTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGCT  >  2:3181256/1‑91                                                                                               GTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGCT  >  2:2528717/1‑91                                                                                               GTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGCT  >  1:3506552/1‑91                                                                                               GTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCAGTCATCGAACTAAGGAGCT  >  2:2528729/1‑91                                                                                                                                                                                           CGATTCGTTTCATGTTAATCCAGCTCCTTAATTCGATGAATGACTTTTAATAGTGATTGTTCAAACACTTTTTGATCTTGCTTTGTAAAAGGTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/754307‑754401 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaggtggTCGCCACAAAGGTCCCCCACCTTTTACAAAGCAAGATCAAAAAGTGTTTGAACAATCACTATTAAAAGTCATTCATCGAATTAAGGAGCT  <  USA300TCH1516_ALE/754417‑754328

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.