New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1858406	132 (0.690)	16 (0.110)	10/126	NT	12.2%	intergenic (‑33/+41)	USA300HOU_RS09235/USA300HOU_RS09240	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 1858419	127 (0.850)					intergenic (‑46/+28)	USA300HOU_RS09235/USA300HOU_RS09240	hypothetical protein/hypothetical protein

CGGTTTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1858300‑1858406 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacaaatgcacttaaatGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAATAAACA  <  USA300TCH1516_ALE/1858419‑1858330                                                                                                                                                                                                       CGGTTTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATA                                                                                                            >  2:2746616/1‑91  GGTTTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAA                                                                                                           >  2:783836/1‑91  GGTTTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAA                                                                                                           >  2:614625/1‑91  GGTTTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAA                                                                                                           >  2:2550285/1‑91    TTTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACA                                                                                                         <  2:1489628/91‑1     TTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAA                                                                                                        <  2:2371974/91‑1     TTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAA                                                                                                        <  2:1982612/91‑1     TTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAA                                                                                                        <  2:1982600/91‑1      TGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAA                                                                                                       >  2:927706/1‑91      TGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAA                                                                                                       >  2:927288/1‑91      TGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAA                                                                                                       <  1:3658258/91‑1       GGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAAT                                                                                                      <  2:1248515/91‑1        GTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATG                                                                                                     >  2:1116121/1‑91         TAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGC                                                                                                    >  1:2001981/1‑91          AGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCA                                                                                                   <  2:2674275/91‑1          AGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCA                                                                                                   >  2:2300727/1‑91           GTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCAC                                                                                                  >  1:2618/1‑91           GTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCAC                                                                                                  <  2:3191507/91‑1           GTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCAC                                                                                                  <  2:1339381/91‑1            TGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACT                                                                                                 <  2:2486808/91‑1            TGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACT                                                                                                 >  1:930074/1‑91              GTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTA                                                                                               <  2:81582/91‑1              GTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTA                                                                                               <  2:311274/91‑1              GTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTA                                                                                               <  2:3675073/91‑1               TTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAA                                                                                              <  1:3517809/91‑1               TTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAA                                                                                              <  2:1923102/91‑1                TCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAA                                                                                             >  1:1424104/1‑91                TCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAA                                                                                             <  2:3332489/91‑1                TCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAA                                                                                             <  1:2822229/91‑1                TCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAA                                                                                             >  1:3662258/1‑91                 CATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAAT                                                                                            >  1:659883/1‑91                 CATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAAT                                                                                            >  1:3663950/1‑91                           AGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTA                                                                                  <  2:523581/91‑1                                GTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTAT                                                                             <  2:3739732/91‑1                                GTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTAT                                                                             <  2:1777836/91‑1                                 TTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATT                                                                            <  1:3242468/91‑1                                 TTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATT                                                                            <  1:1980269/91‑1                                  TTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTT                                                                           <  1:734706/91‑1                                   TATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTA                                                                          <  2:2371879/91‑1                                    ATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTAA                                                                         <  1:2285317/91‑1                                    ATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTAA                                                                         <  2:2850113/91‑1                                    ATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTAA                                                                         <  2:2850009/91‑1                                    ATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTAA                                                                         <  1:3154825/91‑1                                     TTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTAAG                                                                        <  2:14409/91‑1                                     TTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTAAG                                                                        <  1:3415229/91‑1                                        TTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTAAGTGC                                                                     <  1:1102344/91‑1                                         TTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTAAGTGCA                                                                    <  1:413342/91‑1                                                         ATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGAT                                                    <  1:1303997/91‑1                                                                                           AACAAATGCACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAA                  >  2:1084950/1‑91                                                                                             CAAATGCACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACA                >  2:3722424/1‑91                                                                                             CAAATGCACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACA                <  1:40632/91‑1                                                                                               AATGCACTTAAATGAGCTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATAACAAAGCAACAAAATGATAAAAGAACATT              <  2:3708715/91‑1                                                                                                ATGCACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTA             >  2:1781043/1‑91                                                                                                ATGCACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTA             <  2:1551045/91‑1                                                                                                ATGCACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTA             >  1:783836/1‑91                                                                                                ATGCACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTA             >  1:740127/1‑91                                                                                                  GCACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAA           <  1:1568214/91‑1                                                                                                   CACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAA          <  1:2212824/91‑1                                                                                                   CACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAA          <  2:26724/91‑1                                                                                                   CACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAA          <  2:119166/91‑1                                                                                                   CACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAA          >  1:782101/1‑91                                                                                                   CACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAA          >  2:544887/1‑91                                                                                                    ACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAA         >  2:3787179/1‑91                                                                                                    ACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAA         >  1:1146269/1‑91                                                                                                    ACTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAA         >  1:598170/1‑91                                                                                                     CTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAA        <  2:3431134/91‑1                                                                                                     CTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAA        >  2:1866601/1‑91                                                                                                     CTTAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAA        <  1:2890787/91‑1                                                                                                       TAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAtaa      >  2:708950/1‑88                                                                                                       TAAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAATA      <  1:2039384/91‑1                                                                                                        AAATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAATAA     <  1:658036/91‑1                                                                                                          ATGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAATAAAC   <  1:2374056/91‑1                                                                                                           TGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAGAAAATAAACA  >  1:520650/1‑91                                                                                                           TGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAATAAACA  >  1:1310974/1‑91                                                                                                           TGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAATAAACA  >  1:2812492/1‑91                                                                                                                                                                                                       CGGTTTGGTAGTGGTTCATTTTGATAAGTGTGTTTATTTTTTAATGTTCTTTTATCATTTTGTTGCTGCGTCATTTGTATATCCTCCTATAACAAATGCACTTAAAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1858300‑1858406 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacaaatgcacttaaatGAGGTTGTTACTTATTTAAGTGCATTTGTTATAGGAGGATATACAAATGACGCAGCAACAAAATGATAAAAGAACATTAAAAAATAAACA  <  USA300TCH1516_ALE/1858419‑1858330

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.