New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1265511	122 (0.670)	9 (0.060)	9/224	NT	7.3%	intergenic (+19/‑154)	femA_1/dprA	Aminoacyltransferase FemA/DNA processing protein DprA
	?	USA300TCH1516_ALE	= 1265527	120 (0.740)					intergenic (+35/‑138)	femA_1/dprA	Aminoacyltransferase FemA/DNA processing protein DprA

AATGAGGCGGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGAAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1265358‑1265511 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagtatgttggaaaGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTTTAAA  <  USA300TCH1516_ALE/1265527‑1265388                                                                                                                                                                                                                                                                                                        AATGAGGCGGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAA                                                                                                                                                           <  2:720129/141‑1  ATGAGGCGGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAA                                                                                                                                                          >  1:189057/1‑141    GAGGCGGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGT                                                                                                                                                        <  2:1127622/141‑1     gGGCGGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTA                                                                                                                                                       <  2:1079758/140‑1     AGGCGGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTA                                                                                                                                                       <  2:810492/141‑1       GCGGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATG                                                                                                                                                     <  2:1479767/141‑1         GGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTT                                                                                                                                                   >  1:1095222/1‑141         GGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTT                                                                                                                                                   >  3:233485/1‑141           ATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGG                                                                                                                                                 >  1:174317/1‑141           ATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGG                                                                                                                                                 <  2:1303726/141‑1              ATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGAAA                                                                                                                                              >  1:658492/1‑141                TTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGT                                                                                                                                                    <  1:237177/133‑1                TTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGT                                                                                                                                                    >  2:237177/1‑133                            CAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGAAAGAATTTAAAATTTC                                                                                                                                <  2:771603/141‑1                              ATTTAAAAAGGGTTTTAAGGCACATGTTGAAGAATTAATTGGTGGTTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGACAGAATTTAAACTTTCAA                                                                                                                              <  4:578257/141‑1                                TTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGAAAGAATTTAAAATTTCAATT                                                                                                                            <  1:1131469/141‑1                                     AAGGGTTTTAATGCACATGTTGAAGAATTTATTGGTGATTTCAGTAAACAAGTAAGACGAATTCTATATAAAGTTGCAAAACTTATTTATAAAGTTTAATTATAAAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAA                                                                                                                       <  4:408844/141‑1                                              AATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTA                                                                                                              <  3:479860/141‑1                                               ATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTAT                                                                                                             <  1:1326710/141‑1                                                   atATGTTGAAGAATTACTTGGTGGTTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAATGTTTAATTATACAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATT                                                                                                         <  2:1037594/139‑1                                                                      GGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAAC                                                                                                                      >  2:1142873/1‑109                                                                      GGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAAC                                                                                                                      <  1:1142873/109‑1                                                                                                                                            AAAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTA                >  2:1083168/1‑141                                                                                                                                            AAAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTA                >  4:565712/1‑141                                                                                                                                            AAAGTATGATGGAAAGAATTTAAAATTTCAATTTCCAACATAATTTATAATTAAACATTATAAATAAGTTTTACAAATTTATATAGAATTGGTATTACTGGTTTAATGAAATCACCAAATAATTCTTAGAAATGTTCATTA                >  4:572785/1‑141                                                                                                                                             AAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAA               >  2:541901/1‑141                                                                                                                                             AAGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAA               >  3:580927/1‑141                                                                                                                                              AGTATGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAA              >  4:289584/1‑141                                                                                                                                               GTATGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAA             <  1:817909/141‑1                                                                                                                                                  TGTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCC          <  2:581103/141‑1                                                                                                                                                   GTTGGAAATAATATAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCT         <  4:359412/141‑1                                                                                                                                                   GTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCT         <  2:860037/141‑1                                                                                                                                                   GTTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCT         >  3:588948/1‑141                                                                                                                                                    TTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTT        >  3:213349/1‑141                                                                                                                                                    TTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTT        >  2:1130602/1‑141                                                                                                                                                    TTGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTT        <  3:446427/141‑1                                                                                                                                                     TGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTT       <  3:184897/141‑1                                                                                                                                                     TGGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTT       <  1:330632/141‑1                                                                                                                                                      GGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTT      <  2:1138719/141‑1                                                                                                                                                      GGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTT      <  2:1293063/141‑1                                                                                                                                                      GGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTT      >  4:185322/1‑141                                                                                                                                                      GGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTT      <  3:119938/141‑1                                                                                                                                                      GGAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTT      <  1:62936/141‑1                                                                                                                                                       GAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTTT     <  2:980401/141‑1                                                                                                                                                       GAAAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTTT     <  4:378026/141‑1                                                                                                                                                         AAGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAAGCTTATAAATAAGTTCTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTTTAA   <  1:572332/141‑1                                                                                                                                                          AGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTTTAAA  <  2:1003765/141‑1                                                                                                                                                                                                                                                                                                        AATGAGGCGGATGATTTTGGTGTTCAACAATTTAAAAAGGGTTTTAATGCACATGTTGAAGAATTAATTGGTGATTTCATCAAACCAGTAAGACCAATTCTATATAAATTTGCAAAACTTATTTATAAGGTTTAATTATAAAGTATGTTGGAAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1265358‑1265511 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagtatgttggaaaGAATTTAAAATTTCAATTTCCAACATACTTTATAATTAAACCTTATAAATAAGTTTTGCAAATTTATATAGAATTGGTCTTACTGGTTTGATGAAATCACCAATTAATTCTTCAACATGTGCATTAAAACCCTTTTTAAA  <  USA300TCH1516_ALE/1265527‑1265388

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