New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 800994	50 (1.080)	5 (0.110)	4/246	NT	10.0%	intergenic (+128/‑223)	hisC_1/USA300HOU_RS03915	Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase
	?	USA300TCH1516_ALE	= 801032	43 (0.980)					intergenic (+166/‑185)	hisC_1/USA300HOU_RS03915	Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase

CTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGCAACAATAGATGATATTGTTTTGTATCAATT  >  USA300TCH1516_ALE/800894‑801166                                                                                                                                           |                                                                                                                                       cTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCag                                                                                                                                      >  1:475097‑M2/1‑139 (MQ=255)  tttCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCagt                                                                                                                                     >  1:645811‑M2/1‑138 (MQ=255)   ttCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCagtc                                                                                                                                    >  1:644179‑M2/1‑137 (MQ=255)      gCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCagtcaac                                                                                                                                 >  1:556673‑M2/1‑134 (MQ=255)           atttatttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTg                                                                                                                            <  1:643551/141‑1 (MQ=32)           atttatttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTg                                                                                                                            >  1:349606/1‑141 (MQ=32)                tttCGTCCTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAat                                                                                                                       <  2:302186/141‑1 (MQ=21)                  tcgtcgTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAatat                                                                                                                     >  1:623051/1‑141 (MQ=35)                     tcgtcCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAGTCTGGTTGCTCATTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAAc                                                                                                                  >  2:243496/1‑141 (MQ=11)                         cccACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTg                                                                                                              >  1:730074/1‑141 (MQ=35)                          ccACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGt                                                                                                             <  1:43700/141‑1 (MQ=35)                               ccAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGc                                                                                                        <  1:213311/141‑1 (MQ=35)                                  aCTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCAtt                                                                                                     <  2:19560/141‑1 (MQ=37)                                  aCTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCAtt                                                                                                     <  1:149973/141‑1 (MQ=37)                                    ttGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGa                                                                                                   >  1:359467/1‑141 (MQ=38)                                       cATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAACAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACa                                                                                                <  2:233064/141‑1 (MQ=255)                                       cATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACa                                                                                                >  1:459774/1‑141 (MQ=38)                                         ttGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACAtt                                                                                              >  1:504220/1‑141 (MQ=39)                                             cTGTAGAAATTGGGAATCCAATTTCTCTGTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGAtt                                                                                          >  2:61998/1‑141 (MQ=255)                                                tAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTAt                                                                                       <  2:322820/141‑1 (MQ=39)                                                 aGAAATTGGGAATCCAATTTCTCTTTCTTGCGGCGCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTAGTTCAGTCAACTACTGCCAATTTGACTTTGTTGATCATTGAACATTGATTTATg                                                                                      <  2:160122/141‑1 (MQ=11)                                                    aaTTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGtct                                                                                   <  2:70737/141‑1 (MQ=39)                                                     aTTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGtctc                                                                                  <  1:229489/141‑1 (MQ=39)                                                        ggattcccAATTTCTCTTTGTTGGGGCCCCGCCGACAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGACAATATAAATTTGTAGAGCATTGAACATTGATTTATGTCTCAAg                                                                               >  1:189446/7‑141 (MQ=14)                                                         ggAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGc                                                                              >  1:451898/1‑141 (MQ=255)                                                         ggAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGc                                                                              >  2:195985/1‑141 (MQ=255)                                                           aaTCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTc                                                                            <  2:69202/141‑1 (MQ=255)                                                            aTCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCa                                                                           >  1:486359/1‑141 (MQ=40)                                                            aTCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTGGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCa                                                                           >  1:568682/1‑141 (MQ=255)                                                                aaTTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGc                                                                       <  1:382703/141‑1 (MQ=255)                                                                     ctctTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTAAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAgtgt                                                                  <  1:75464/141‑1 (MQ=255)                                                                      tctTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGtgtg                                                                 >  2:305934/1‑141 (MQ=255)                                                                          tgttgGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAatg                                                             <  1:458526/141‑1 (MQ=255)                                                                                 gCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAggg                                                      >  1:739434/1‑140 (MQ=255)                                                                                    ccgccgGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGAGTGAATGATAAGGTgag                                                   >  1:775485/1‑141 (MQ=255)                                                                                     cgccgGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTgaga                                                  <  1:81814/141‑1 (MQ=255)                                                                                              ggTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAgt                                         >  1:448151/1‑141 (MQ=255)                                                                                                ttGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCagtcaactactgccggcggggccccaacaaagagaaattggattcccaatttctacagacaatgcaagttggggtgggacgacgaaataaattttac                                       <  1:49397‑M2/141‑98 (MQ=255)                                                                                                   aCTAGAATTGAAAACAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGATTATTCAGTGTaaa                                    <  1:342224/141‑1 (MQ=255)                                                                                                   aCTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCagtcaaccttgccggcggggccccaacaaagagaaattggattcccaatttctacagacaatgcaagttggggtgggacgacgaaataaattttgcgaaa                                    <  1:222914‑M2/141‑101 (MQ=255)                                                                                                    cTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCagtcaaccttgccggcggggccccaacaaagagaaattggattcccaatttctacagacaatgcaagttggggtgggacgacgaaataaattttgcgaaag                                   <  2:144749‑M2/141‑102 (MQ=255)                                                                                                       gAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGc                                >  1:349206/1‑141 (MQ=255)                                                                                                       gAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGc                                >  2:38954/1‑141 (MQ=255)                                                                                                        aaTTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCagtcaaccttgccggcggggccccaacaaagagaaattagattcccaatttctacagacaatgcaagttgggtcgcgacaaagaaataaattttgcgaaagtatc                               <  1:425506‑M2/141‑106 (MQ=255)                                                                                                          ttGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGcaac                             <  2:142475/141‑1 (MQ=255)                                                                                                          ttGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGcaac                             <  2:60479/141‑1 (MQ=255)                                                                                                          ttGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACAGTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGcaac                             <  1:47918/141‑1 (MQ=255)                                                                                                               aaaaGCTTGTTACAAGCGCATTTTCGTTCagtcaaccttgccggcggggccccaacaaagagaaattggattcccaatttctacagacaatgcaagttggggtgggacgacgaaataaattttgcgaaagtatcatttctg                        <  1:62076‑M2/141‑113 (MQ=255)                                                                                                                 aaGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGACAGTATTCAGTGTAAAAAGCAACAATAgat                      <  1:537209/141‑1 (MQ=255)                                                                                                                             aGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGCAACAATAGATGATATTGTTTTg          <  1:160678/141‑1 (MQ=255)                                                                                                                              gcgcATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGCAACAATAGATGATATTGTTTTGt         >  1:323596/1‑141 (MQ=255)                                                                                                                                    tttCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGCAACAATAGATGATATTGTTTTGTATCAAt   >  1:19408/1‑141 (MQ=255)                                                                                                                                     ttCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGCAACAATAGATGATATTGTTTTGTATCAAtt  <  2:334332/141‑1 (MQ=255)                                                                                                                                     ttCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGCAACAATAGATGATATTGTTTTGTATCAAtt  <  2:219048/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                       CTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAAGCTCAATGCAGTGTGAATGATGAGGTGAGAGTATTCAGTGTAAAAAGCAACAATAGATGATATTGTTTTGTATCAATT  >  USA300TCH1516_ALE/800894‑801166

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.