New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 885389	93 (0.950)	15 (0.180)	10/134	NT	15.8%	intergenic (+18/+55)	pspB/argO	Putative phosphoserine phosphatase 2/Arginine exporter protein ArgO
	?	USA300TCH1516_ALE	= 885408	82 (1.000)					intergenic (+37/+36)	pspB/argO	Putative phosphoserine phosphatase 2/Arginine exporter protein ArgO

TAATATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/885287‑885389 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagcgttatacaAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATTGTCATATT  <  USA300TCH1516_ALE/885408‑885319                                                                                                                                                                                                   TAATATCGGGAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATA                                                                                                        <  1:3973093/91‑1  AATATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAA                                                                                                       >  1:976092/1‑91  AATATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAA                                                                                                       <  1:217280/91‑1  AATATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAA                                                                                                       <  1:181356/91‑1   ATATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAA                                                                                                      >  1:1105658/1‑91   ATATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAA                                                                                                      >  1:980214/1‑91   ATATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAA                                                                                                      <  1:662306/91‑1   ATATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAA                                                                                                      <  1:2606149/91‑1    TATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAG                                                                                                     >  1:2419931/1‑91     ATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGC                                                                                                    <  1:1873970/91‑1     ATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGC                                                                                                    >  1:4088579/1‑91     ATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGC                                                                                                    >  1:4088591/1‑91       CGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGT                                                                                                  >  1:3411597/1‑91        GGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTT                                                                                                 <  1:305645/91‑1        GGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTT                                                                                                 >  1:3266756/1‑91             TTGTAATGTCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAATCGTTATACA                                                                                            <  1:2088025/91‑1             TTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACA                                                                                            >  1:1982675/1‑91                        TGAAATTTGAATATGACAATGGAACTTTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACT                                                                                 <  1:3874548/91‑1                                 AATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTAT                                                                        <  1:1627504/91‑1                                  ATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATG                                                                       <  1:511211/91‑1                                  ATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATG                                                                       <  1:2737737/91‑1                                     TGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTAT                                                                    <  1:3443348/91‑1                                     TGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTAT                                                                    <  1:2601698/91‑1                                     TGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTAT                                                                    <  1:2601777/91‑1                                     TGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTAT                                                                    <  1:2602166/91‑1                                      GACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTATA                                                                   <  1:741871/91‑1                                      GACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTATA                                                                   <  1:3224861/91‑1                                       ACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTATAA                                                                  <  1:528145/91‑1                                         AATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTATAACG                                                                <  1:3667040/91‑1                                                  TTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTA                                                       <  1:1443914/91‑1                                                   TTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTAT                                                      <  1:1314290/91‑1                                                     AAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTA                                                    <  1:836117/91‑1                                                                                            AAGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCC             >  1:2587798/1‑91                                                                                            AAGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCC             >  1:3419699/1‑91                                                                                            AAGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCC             <  1:20906/91‑1                                                                                            AAGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCC             <  1:20761/91‑1                                                                                             AGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCA            >  1:1290472/1‑91                                                                                             AGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCA            <  1:1140744/91‑1                                                                                             AGCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCA            >  1:1378236/1‑91                                                                                              GCGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCAT           <  1:139825/91‑1                                                                                               CGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATT          >  1:1219831/1‑91                                                                                               CGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATT          >  1:2390862/1‑91                                                                                               CGTTATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATT          >  1:3069374/1‑91                                                                                                   ATACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATTGTCA      >  1:1266386/1‑91                                                                                                     ACAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATTGTCATA    <  1:2191080/91‑1                                                                                                      CAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATTGTCATAT   <  1:2040818/91‑1                                                                                                      CAAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATTGTCATAT   <  1:1733848/91‑1                                                                                                       AAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATTGTCATATT  <  1:1031216/91‑1                                                                                                                                                                                                   TAATATCGGTAATTGTAATATCCTGAAATTTGAATATGACAATGGAACATTTAAATTTGTTGAGTTAATTGATCCAAATTTATAATAAATAAAGCGTTATACA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/885287‑885389 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagcgttatacaAAAGACATACTTGTGTCTATGTATAACGCTTTATTTATTATAAATTTGGATCAATTAACTCAACAAATTTAAATGTTCCATTGTCATATT  <  USA300TCH1516_ALE/885408‑885319

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