New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1834069	142 (0.700)	8 (0.050)	5/138	NT	6.0%	intergenic (+18/‑96)	osmC/USA300HOU_RS09140	Peroxiredoxin OsmC/Soluble hydrogenase 42 kDa subunit
	?	USA300TCH1516_ALE	= 1834086	130 (0.740)					intergenic (+35/‑79)	osmC/USA300HOU_RS09140	Peroxiredoxin OsmC/Soluble hydrogenase 42 kDa subunit

TTGCAGATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1833969‑1834069 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagtgataacgCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTACAGC  <  USA300TCH1516_ALE/1834086‑1833998                                                                                                                                                                                                TTGCAGATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTA                                                                                                     <  2:2862379/91‑1  TGCAGATAATAATTGCATGATTTCAAATGCTGTAAGAGATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAA                                                                                                    >  1:3334413/1‑91  TGCAGATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAA                                                                                                    >  1:2626441/1‑91  TGCAGATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAA                                                                                                    >  1:860047/1‑91   GCAGATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAG                                                                                                   >  1:2564922/1‑91   GCAGATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAG                                                                                                   <  1:2019420/91‑1    CAGATAATAATTGCATGATTTCAAATGCTGTAAGAACTAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGT                                                                                                  <  2:3903206/91‑1    CAGATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGT                                                                                                  <  1:1157237/91‑1     AGATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTG                                                                                                 >  1:2244466/1‑91       ATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGAT                                                                                               <  1:374172/91‑1       ATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGAT                                                                                               <  1:132771/91‑1        TAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTTTCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATA                                                                                              <  1:3343213/91‑1        TAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATA                                                                                              <  1:960618/91‑1        TAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATA                                                                                              >  2:1542866/1‑91        TAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATA                                                                                              <  2:2275683/91‑1        TAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATA                                                                                              <  2:2608191/91‑1        TAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATA                                                                                              >  1:104083/1‑91        TAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATA                                                                                              >  1:2020781/1‑91        TAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATA                                                                                              <  1:1337021/91‑1        TAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATA                                                                                              <  1:1945410/91‑1         AATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAA                                                                                             >  1:1134689/1‑91         AATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAA                                                                                             <  2:3319736/91‑1          ATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAAC                                                                                            >  1:2565519/1‑91          ATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAAC                                                                                            >  1:2565520/1‑91           TAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACCTAAAAATCTATCCCATCATTCAGGCGAAATAAAATCGTTAAGTGATAACG                                                                                           >  2:3664802/1‑91           TAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACG                                                                                           <  2:1826649/91‑1           TAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACG                                                                                           <  2:1024490/91‑1           TAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACG                                                                                           <  2:3694162/91‑1                            ATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACGCTATATTGTCGAACAAA                                                                          <  2:858493/91‑1                            ATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACGCTATATTGTCGAACAAA                                                                          <  2:2425698/91‑1                            ATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACGCTATATTGTCGAACAAA                                                                          <  1:1018861/91‑1                               CTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACGCTATATTGTCGAACAAACGT                                                                       <  1:973334/91‑1                               CTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACGCTATATTGTCGAACAAACGT                                                                       <  1:974143/91‑1                                TGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACGCTATATTGTCGAACAAACGTT                                                                      <  2:63728/91‑1                                  TAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACGCTATATTGTCGAACAAACGTTAT                                                                    <  2:1979139/91‑1                                     GAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACGCTATATTGTCGAACAAACGTTATCAC                                                                 <  1:784050/91‑1                                                                                           AAGTGATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATT           >  1:647737/1‑91                                                                                           AAGTGATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATT           >  1:1576259/1‑91                                                                                            AGTGATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTT          <  1:537814/91‑1                                                                                             GTGATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTC         >  1:1305279/1‑91                                                                                             GTGATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTC         <  2:1479797/91‑1                                                                                             GTGATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTC         <  2:440663/91‑1                                                                                              TGATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCT        >  1:1900960/1‑91                                                                                              TGATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCT        >  1:2648038/1‑91                                                                                               GATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTT       >  2:623121/1‑91                                                                                               GATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTT       >  2:153130/1‑91                                                                                               GATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTT       >  2:3810899/1‑91                                                                                                ATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGTATGATGGGATAGATTTTTATGTCCACATTATTTCTTA      <  1:3343168/91‑1                                                                                                ATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTA      >  2:2779145/1‑91                                                                                                ATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTA      >  2:2778975/1‑91                                                                                                ATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTA      >  1:2021675/1‑91                                                                                                ATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTA      <  2:1817727/91‑1                                                                                                ATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTA      >  1:1540687/1‑91                                                                                                ATAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTA      >  1:2031555/1‑91                                                                                                 TAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTAC     <  1:955715/91‑1                                                                                                 TAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTAC     <  1:1754635/91‑1                                                                                                 TAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTAC     <  1:615518/91‑1                                                                                                 TAACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTAC     >  1:342981/1‑91                                                                                                  AACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTACA    <  1:4067/91‑1                                                                                                  AACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTACA    <  2:545801/91‑1                                                                                                   ACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTACAG   >  1:912026/1‑91                                                                                                   ACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTACAG   >  1:898420/1‑91                                                                                                   ACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTACAG   >  1:1914956/1‑91                                                                                                   ACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTACAG   <  2:964913/91‑1                                                                                                   ACGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGACATTTATGTCCACATTATTTCTTACAG   >  2:3418188/1‑91                                                                                                    CGCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTACAGC  >  2:2162372/1‑91                                                                                                                                                                                                TTGCAGATAATAATTGCATGATTTCAAATGCTGTAAGAAATAATGTGGACATAAAAATCTATCCCATCATTCAGGCCAAATAAAATCGTTAAGTGATAACG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1833969‑1834069 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagtgataacgCTATATTGTCGAACAAACGTTATCACTTAACGATTTTATTTGGCCTGAATGATGGGATAGATTTTTATGTCCACATTATTTCTTACAGC  <  USA300TCH1516_ALE/1834086‑1833998

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.