New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 891804	45 (0.970)	4 (0.090)	3/250	NT	8.9%	intergenic (+222/‑517)	USA300HOU_RS04385/rnmV_2	hypothetical protein/Ribonuclease M5
	?	USA300TCH1516_ALE	= 2031829	39 (0.880)					intergenic (+295/+195)	USA300HOU_RS10250/USA300HOU_RS10255	hypothetical protein/hypothetical protein

CAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTATTTAAAAATAGGAAT  >  USA300TCH1516_ALE/891664‑891943                                                                                                                                              |                                                                                                                                            cAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATGTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACT                                                                                                                                             <  1:641952‑M1/141‑1 (MQ=255)  aaaaTTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTa                                                                                                                                            <  2:154642/141‑1 (MQ=40)  aaaaTTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTa                                                                                                                                            >  2:247133/1‑141 (MQ=255)        tatttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTg                                                                                                                                      <  2:199222/141‑1 (MQ=255)         atttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGa                                                                                                                                     <  1:33300/141‑1 (MQ=40)         atttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGa                                                                                                                                     <  1:308361/141‑1 (MQ=255)           ttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGaaa                                                                                                                                   <  1:126930/141‑1 (MQ=40)                             cTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAgcgc                                                                                                                 >  1:689461/1‑141 (MQ=255)                               tGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCAt                                                                                                               <  2:272618/141‑1 (MQ=255)                                 cATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTagaattgaaaatgcgcttgtaacaagcttttt                                                                                                             <  1:334828‑M1/141‑33 (MQ=255)                                  aTTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTCGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTATGTTGGGGCCCCTGACTgaacgaaaatgcgcttgtaacaagcttttttc                                                                                                             <  1:248756‑M1/141‑33 (MQ=255)                                    tGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTATAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCg                                                                                                          <  2:30393/141‑1 (MQ=255)                                    tGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCg                                                                                                          >  1:255011/1‑141 (MQ=255)                                      tCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTagaattgaaaatgcgcttgtaacaagcttttttcaat                                                                                                        <  1:173113‑M1/141‑38 (MQ=255)                                        tGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTagaattgaaaatgcgcttgtaacaagcttttttcaattc                                                                                                      <  2:10665‑M1/141‑40 (MQ=255)                                         gTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAAATTGCATTGACTGTCGCCATTTTTTACGCTGCGTCCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAg                                                                                                     <  2:283352/141‑1 (MQ=14)                                          tAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGt                                                                                                    >  1:472894/1‑141 (MQ=255)                                                 tGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAactac                                                                                             >  1:577426/1‑141 (MQ=255)                                                 tGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAactac                                                                                             <  1:142567/141‑1 (MQ=255)                                                   gattcccAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTg                                                                                           >  1:152443/6‑141 (MQ=255)                                                      aTCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCa                                                                                        >  1:410181/1‑141 (MQ=255)                                                       tCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCaa                                                                                       <  2:108340/141‑1 (MQ=255)                                                          aaTTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAatat                                                                                    <  1:280325/141‑1 (MQ=255)                                                              tctcTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACt                                                                                <  1:304107/141‑1 (MQ=255)                                                                 ctTTGTTGGGGCCCA‑TCCCCAACTTGCCTTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATNTTCGTTCAGTCAACTNCTGCCAATATAACTTCg                                                                             <  1:740310/141‑1 (MQ=255)                                                                    tgttgGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACACGCACATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTag                                                                          >  2:49366/1‑141 (MQ=255)                                                                         gggCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGGTGGTGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCAt                                                                     >  1:473829/1‑141 (MQ=255)                                                                          ggCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATa                                                                    <  1:512687/141‑1 (MQ=38)                                                                          ggCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATa                                                                    <  1:331243/141‑1 (MQ=38)                                                                           gCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAg                                                                   >  1:16306/1‑141 (MQ=38)                                                                           gCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAg                                                                   >  1:153953/1‑141 (MQ=38)                                                                               a‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACa                                                               >  1:127836/1‑141 (MQ=34)                                                                               a‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACa                                                               >  1:127817/1‑141 (MQ=34)                                                                                 tCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATCACTTCGTAGAGCATAGAACAt                                                              >  1:132756/1‑141 (MQ=18)                                                                                  ccccAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACCAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACAtt                                                             >  2:138151/1‑141 (MQ=17)                                                                                     cAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGAt                                                          <  1:349364/141‑1 (MQ=32)                                                                                          tGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATg                                                     <  2:205416/141‑1 (MQ=32)                                                                                               tGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCa                                                <  2:47239/141‑1 (MQ=32)                                                                                                gCCTGTAGAATTTCTTTTCCTGATGCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAg                                               <  2:169356/141‑1 (MQ=255)                                                                                                 ccTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGc                                              <  2:133131/141‑1 (MQ=32)                                                                                                    gTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTg                                           <  2:194130/141‑1 (MQ=32)                                                                                                    gTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTg                                           <  1:551202/141‑1 (MQ=17)                                                                                                        aaTTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGtttt                                       <  1:87589/141‑1 (MQ=35)                                                                                                        aaTTTCTTTTCGAAATTCTCGGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGtttt                                       <  1:644315/141‑1 (MQ=25)                                                                                                               aaaagAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGc                                >  2:133558/5‑141 (MQ=255)                                                                                                                        tctcTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTaa                       >  1:421079/1‑141 (MQ=255)                                                                                                                             gtgtTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATgtgt                  <  2:49871/141‑1 (MQ=255)                                                                                                                             gtgtTGGGGCCCCTGACTAGAATTGAAAAAAGCTATTTGCAAGCGCATTTTCGTTCAGTCAACTACTGCCAAAAAAACTTCGTAGAGCATAGTACATTTTTATATGGCCCAGCCTCTTTTCATAAGCCCCAGCTaaaccgt                  >  1:403173/1‑136 (MQ=14)                                                                                                                               gtTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTAt                <  1:540349/141‑1 (MQ=255)                                                                                                                                 tGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACACGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTAttt              <  2:17064/141‑1 (MQ=255)                                                                                                                                  ggggCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTATTTa             >  1:357804/1‑141 (MQ=255)                                                                                                                                         cTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTATTTAAAAATAg      <  1:576526/141‑1 (MQ=255)                                                                                                                                          tgactgaacgaaaatgcgcttgtaacaagcttttttcaattctagtcaggggccccaacaaagagaaattggattcccaatttctacagacaatgcaagttggggtgtgggccccaacaaagagaaattggattcccaatt     <  1:402418‑M1/141‑137 (MQ=255)                                                                                                                                          tGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTATTTAAAAATAgg     <  1:712075/141‑1 (MQ=255)                                                                                                                                          tGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTATTTAAAAATAgg     >  1:129470/1‑141 (MQ=255)                                                                                                                                           gactgaacgaaaatgcgcttgtaacaagcttttttcaattctagtcaggggccccaacaaagagaaattggattcccaatttctacagacaatgcaagttggggtgtgggccccaacaaagagaagttggattcccaattt    >  1:654066‑M1/1‑4 (MQ=255)                                                                                                                                           gactgaacgaaaatgcgcttgtaacaagcttttttcaattctagtcaggggccccaacaaagagaaattggattcccaatttctacagacaatgcaagttggggtgtgggccccaacaaagagaaattggattcccaattt    >  1:611591‑M1/1‑4 (MQ=255)                                                                                                                                            aCTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTATTTAAAAATAGGaa   >  1:593910/1‑141 (MQ=255)                                                                                                                                             cTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTATTTAAAAATAGGAAt  >  2:298492/1‑141 (MQ=255)                                                                                                                                              |                                                                                                                                            CAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCA‑TCCCCAACTTGCATTGCCTGTAGAATTTCTTTTCGAAATTCTCTGTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCAGCCTGTTTTCATAAGCCACAGCTAATGTGTATTTAAAAATAGGAAT  >  USA300TCH1516_ALE/891664‑891943

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.