New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 800928	43 (0.840)	7 (0.150)	6/246	NT	14.8%	intergenic (+62/‑289)	hisC_1/USA300HOU_RS03915	Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase
	?	USA300TCH1516_ALE	801948 =	40 (0.830)					intergenic (+189/+435)	USA300HOU_RS03915/USA300HOU_RS03920	Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase

GGTGTTAGAATTACAATTGGTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCA  >  USA300TCH1516_ALE/800789‑801065                                                                                                                                            |                                                                                                                                          ggTGTTAGAATTACAATTGGTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACt                                                                                                                                          <  1:344165/141‑1 (MQ=255)  gtaatataaTTACAAGTGGGTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGTACAGAAATGATACTTTCGCAAAATCTATTTCGTCGTCCCACCCCAACtt                                                                                                                                         <  2:30117/134‑1 (MQ=37)   tgtTAGAATTACAATTGGTTTTAAAGAACAAAATGATAAAATAATACAGTAGTGATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACtta                                                                                                                                        <  2:135361/141‑2 (MQ=25)           ttACAATTGGTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACataaagaaata                                                                                                                                <  1:432014‑M1/141‑12 (MQ=255)           ttACAATTGGTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAAAataaataaata                                                                                                                                >  2:544021‑M1/1‑130 (MQ=255)                    gTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAAtt                                                                                                                       >  2:612570/1‑141 (MQ=255)                    gTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAAATTGCATTGTCTGTAGAAAtt                                                                                                                       >  2:289673/1‑141 (MQ=255)                      tttAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTgg                                                                                                                     <  2:255108/141‑1 (MQ=255)                        tAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGa                                                                                                                   >  1:70082/1‑141 (MQ=255)                          aaGAACAAGATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACataaagaaatactttttctttagaaa                                                                                                                 <  1:414769‑M1/141‑27 (MQ=255)                          aaGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAAt                                                                                                                 >  1:13358/1‑141 (MQ=255)                          aaGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCACAACataaagaaatactttttctttagaaa                                                                                                                 <  1:93893‑M1/141‑27 (MQ=255)                             aaCAAAATGATAAACTGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCa                                                                                                              >  1:214650/1‑141 (MQ=255)                             aaCAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACataaagaaatactttttctttagaaatta                                                                                                              >  2:626230‑M1/1‑112 (MQ=255)                             aaCAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCa                                                                                                              <  1:72958/141‑1 (MQ=255)                             aaCAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCa                                                                                                              <  1:169947/141‑1 (MQ=255)                             aaCAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCa                                                                                                              <  2:18810/141‑1 (MQ=255)                             aaCAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGCGCCAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCa                                                                                                              <  1:150209/141‑1 (MQ=255)                              aCAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTAGGACAGAAATGATACTTTCGCAAAATTTATTTCGTAGTCCCACCCCAACTTGCCTTGTCTGTAGACATTCGGAAcccca                                                                                                             >  2:332330/1‑139 (MQ=25)                                     gATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGCAATTGGGAATCCAATTTctct                                                                                                      >  2:203791/1‑141 (MQ=255)                                     gATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTctct                                                                                                      >  1:546591/1‑141 (MQ=255)                                                 gAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGccc                                                                                          <  1:597157/141‑1 (MQ=255)                                                   aGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCccg                                                                                        >  1:74060/1‑141 (MQ=255)                                                       ttATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCACCTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCgg                                                                                    >  1:361597/1‑141 (MQ=255)                                                       ttATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCgg                                                                                    >  1:517325/1‑141 (MQ=255)                                                        tATCAAACTTTTATCATTAATAGTAAGTGGGGAGTTGGGCATAAATGATAATTTCTCATTGGGTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGc                                                                                   <  2:105253/141‑1 (MQ=14)                                                        tATCAAACTTTAAAGACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCGGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGc                                                                                   <  2:75777/141‑1 (MQ=255)                                                               cTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTg                                                                            <  1:583581/141‑1 (MQ=255)                                                                tttAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATGCTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGa                                                                           >  1:451344/1‑141 (MQ=255)                                                                tttAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTgc                                                                           >  1:528668/1‑140 (MQ=255)                                                                   aaaTACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACataaagaaatactttttctttagaaattagtatttcttatgcatgagtgtaactcatgcattcatat                                                                        >  1:11567‑M1/1‑74 (MQ=255)                                                                     aTACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGa                                                                      <  1:127182/141‑1 (MQ=255)                                                                         gAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTg                                                                  >  1:345678/1‑141 (MQ=255)                                                                         gAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAACTTCTATTTGTTCGGGCCCCGCCGGCAAGGTTGACTAGAATTg                                                                  >  1:569616/1‑141 (MQ=255)                                                                           aTAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGaa                                                                <  2:345678/141‑1 (MQ=255)                                                                              gTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGcaaaa                                                             >  1:618926/1‑141 (MQ=255)                                                                                           gggACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCAAATTTCACTTTGTTGTGGCCCCGCCTGTTAGTTTAACTACAATTGAAAAAAGCTTGTTACAAg                                                >  2:104762/1‑141 (MQ=14)                                                                                            ggACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACGCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCGAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAgc                                               >  1:94018/1‑141 (MQ=255)                                                                                              aCAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAgcgc                                             <  1:39782/141‑1 (MQ=39)                                                                                                aGAAATGATACTTTCGCAAAATTTATTTCGGCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCAt                                           <  2:103113/141‑1 (MQ=255)                                                                                                 aaaaTGATAGTTTCGCAAAATTTATTTCGTCGTGCCACCCCGACTTGCAGTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAGGCGCAtt                                          <  2:103998/140‑1 (MQ=11)                                                                                                      gATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGAAAAAAAAAAAAAAAAGCTTGTTACAAGCGCATTTTCGt                                     <  2:70082/141‑1 (MQ=14)                                                                                                       aTACTTTCGCAAAATTTATTTCGTCGTCCCCCCCCAACAGAGATTGCCGATAGAAAGTGGGAGTAATATTTCTTTTTGTTGGGGCCCCGACGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATGTTCGtt                                    >  1:304686/1‑141 (MQ=14)                                                                                                           tttCGCAAAATTTATTTCGTGGACGCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGt                                <  2:1423/141‑1 (MQ=255)                                                                                                            ttCGTAAAAGTTATTTCGTCGTCTCTCCCCAACTTGCATTGTCTGTAGAAATTGCGAATCCAATTTCGCTTTGTTGGGTCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAACCTTGTTACAAGCGCATTTTCGTTCAGTc                               <  2:324821/141‑1 (MQ=11)                                                                                                            ttCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTc                               >  1:251187/1‑141 (MQ=37)                                                                                                             tCGGAAAATTTATTTCGTCGTCCCATCCAAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCa                              <  2:158815/141‑1 (MQ=12)                                                                                                                cAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAact                           >  1:377045/1‑141 (MQ=33)                                                                                                                    atttatttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTg                       >  1:615668/1‑141 (MQ=32)                                                                                                                    atttatttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTg                       >  1:640005/1‑141 (MQ=32)                                                                                                                         tttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCAATTTCGTTCAGTCAACTACTGCCAat                  >  1:352839/1‑141 (MQ=18)                                                                                                                            cgtcgtCCCACCCCAACTTGCATTGTCTGTCGAAATTGGGAATCCAATTTCTCTTTGTTGGGGACAAGCCGGCTAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTCCTGCCAAtata               >  1:243555/1‑141 (MQ=11)                                                                                                                               cgtcCCACCCCAACataaagaaatactttttctttagaaattagtatttcttatgcatgagtgtaactcatgcattcatatttttaagtacacattagctgtgactaatgataaagaatcgctacataatcaatcattagt            <  1:626230‑M1/141‑128 (MQ=255)                                                                                                                                         cAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCa  <  2:74060/141‑1 (MQ=35)                                                                                                                                            |                                                                                                                                          GGTGTTAGAATTACAATTGGTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCA  >  USA300TCH1516_ALE/800789‑801065

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.