New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2660570 =	42 (0.920)	4 (0.100)	4/234	NT	10.1%	intergenic (+12/+237)	ldhD_1/ybiV	D‑lactate dehydrogenase/Sugar phosphatase YbiV
	?	USA300TCH1516_ALE	2660603 =	33 (0.800)					intergenic (+45/+204)	ldhD_1/ybiV	D‑lactate dehydrogenase/Sugar phosphatase YbiV

CTGATGAAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATATTTGATGA  >  USA300TCH1516_ALE/2660467‑2660737                                                                                                                                         |                                                                                                                                       ctGATGAAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGTCATGTGCCTTTGCTTTTTAtt                                                                                                                                     <  1:282748/140‑1 (MQ=255)   gatgaAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAAGATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTAtttt                                                                                                                                   >  2:376829/1‑140 (MQ=255)    atgaAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTg                                                                                                                                  >  2:51493/1‑140 (MQ=255)     tgaAGCAGTACAAAACCTTGTTGAAGGTGGTTGAAACGTAGCTTTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATCTTGt                                                                                                                                 <  1:374236/140‑1 (MQ=255)        aGCAGTACAAAACCTTATTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTTAAAAACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCATTTGATTTTTATTTTGtata                                                                                                                              >  1:292967/1‑140 (MQ=255)           aGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCt                                                                                                                           >  1:60913/1‑140 (MQ=255)             tACACAGCCGTGTTGAAGGTGTTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGt                                                                                                                         <  2:154892/140‑1 (MQ=255)             tACAAAACCTTGGTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGt                                                                                                                         <  2:154908/140‑1 (MQ=255)                 aaaCCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGGTTTTTATTTTGTATATCTGTATCa                                                                                                                     >  2:55085/1‑140 (MQ=255)                  agccTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGGATATCTGtcgcat                                                                                                                    <  2:93576/138‑6 (MQ=255)                    tcTTGTTGAAGTGGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGTAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCaaaa                                                                                                                  <  2:319387/139‑1 (MQ=255)                     cTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAAt                                                                                                                 <  1:549505/140‑1 (MQ=255)                      ttgttgAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTCAATGAAGACGCACACCTTGTGCCTTTGCTTTTTATTTTGTATATCTGTATCACAATc                                                                                                                >  1:483138/1‑140 (MQ=255)                      ttgttgAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAACAta                                                                                                                >  2:135075/1‑139 (MQ=255)                         ttgAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGAt                                                                                                             <  1:528291/140‑1 (MQ=255)                             actaaaatcatttgaatagatgataaaataaagcggattttaatcaaatcgattttgatacagatatacaaaataaaaagcaaaggcgcgccatgtgcctttgctcttTATTTTGTATATCTGTATCAAAATCGATTTGa                                                                                                         <  1:348878‑M2/32‑1 (MQ=255)                               taaattcatttgaatagataataaaattaagcggattctaatcaaatcgattttgatacatatatacaaaataaaaatcaaatgcacatggcgcgcctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGAtt                                                                                                       <  2:180755‑M2/34‑1 (MQ=255)                                tggtTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTa                                                                                                      <  1:109315/140‑1 (MQ=255)                                 tgtTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTaa                                                                                                     <  1:363822/139‑1 (MQ=255)                                  gtTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTaaa                                                                                                    <  2:67267/140‑1 (MQ=255)                                     tAAACGCAGCCTTATCTGTCATTAACACTGGTACAAAGGATACACGGTTACATTGTCATAGACATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCAATTTGATTAAAATc                                                                                                 >  1:129298/1‑140 (MQ=255)                                     tAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAACAAAAGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATc                                                                                                 >  1:280270/1‑140 (MQ=255)                                              caTTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATTTTTTTAATAGCTTTGGCGCGCCTTGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCtttatt                                                                                        <  1:197282/140‑1 (MQ=255)                                                          ttAACACTGGTACATGGGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTAtt                                                                            <  2:79803/140‑1 (MQ=255)                                                           tAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTc                                                                           >  2:445745/1‑140 (MQ=255)                                                                     aCAGGTGAAACACGTTTAAATCAATTTATATATTTAAAAGCAAAGGCGCGCCATTTGTCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCACCTATTCAAATGAtttt                                                                 <  1:283198/140‑1 (MQ=255)                                                                      aatcaaatcgattttgatacagatatacaaaataAAAAGCAAAGGCGCGCCATGTGCATTTGATTTTTATTTTGTATATATGTATCAAAATCGATTTGATTAGAATCCGCTTAATTTTATTATCTATTCAAATGAATTTa                                                                <  2:180755‑M1/106‑1 (MQ=255)                                                                        tcaaatcgattttgatacagatatacaaaataAAGAGCAAAGGCACATGGCGCGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGt                                                              <  1:348878‑M1/108‑1 (MQ=255)                                                                         gtgAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTTTTTTATCTTGTATTCAAATGATTTTAGTg                                                             >  2:247841/1‑140 (MQ=255)                                                                             atcacGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGTCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCt                                                         <  1:81267/138‑1 (MQ=255)                                                                             aaCACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCt                                                         >  1:31035/1‑140 (MQ=255)                                                                                acGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTAt                                                      <  1:458455/140‑1 (MQ=255)                                                                                acGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTAt                                                      >  1:330842/1‑140 (MQ=255)                                                                                  gTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTAttt                                                    >  1:276675/1‑140 (MQ=255)                                                                                         ttAATATATATATTTAAAACCAAAGGCGCGCCATTTCCTTTTGCTTTTTATTTTGTATATCTTCATCAAAATCGATTTGCTTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATg                                             <  2:236943/140‑1 (MQ=255)                                                                                                    atTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGcc                                  <  2:63352/140‑1 (MQ=255)                                                                                                          aggcaaaggcacatggctcgtctttgtttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCt                            <  2:348878‑M2/109‑1 (MQ=255)                                                                                                          AAGCAAAGGCGTGCCATGTGCTTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCt                            >  1:41305‑M1/1‑140 (MQ=255)                                                                                                           AGCAAGGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATTTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTGAGTGCGGTTATTTTACTATGGCATTAGTGCCTAACCTg                           >  1:13576‑M1/1‑140 (MQ=255)                                                                                                            GCAAAGGCGCGCCATGTGCCTTTTCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGt                          >  1:51493‑M1/1‑140 (MQ=255)                                                                                                             CAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGtt                         <  1:484242‑M1/140‑1 (MQ=255)                                                                                                                AGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAAGCTGTTTga                      <  2:211960‑M1/140‑1 (MQ=255)                                                                                                                  GCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTgaga                    <  2:110056‑M1/140‑1 (MQ=255)                                                                                                                    acatggcgcgcctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGata                  >  2:362677‑M2/22‑140 (MQ=255)                                                                                                                     cgcCATGTGCCTTTGCTTTTTATTTTGTATATCTGTCTCATAATCGATATGATTATAATCCGGTTTATTTTATCATCTATTCAAATGCTTTTAGGTCGCTTATTTTACTATGGCCTTATTGCCTAACCTGTTTGAGatat                 >  2:227647/1‑140 (MQ=255)                                                                                                                     cgcCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGatat                 >  1:471109/1‑140 (MQ=255)                                                                                                                              cctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGTTTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATAtt        <  1:199709‑M2/129‑1 (MQ=255)                                                                                                                              cctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATAtt        <  2:521241‑M2/129‑1 (MQ=255)                                                                                                                              cctttgcttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTACCATCTATTCAAATGATTTTATTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATAtt        <  2:442575‑M2/129‑1 (MQ=255)                                                                                                                                    cttttTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATATTtgttga  >  2:506494‑M2/6‑140 (MQ=255)                                                                                                                                         |                                                                                                                                       CTGATGAAGCAGTACAAAACCTTGTTGAAGGTGGTTTAAACGCAGCATTATCTGTCATTAACACTGGTACATGTGAAACACGTTTAAATTAATATATATATTTAAAAGCAAAGGCGCGCCATGTGCCTTTGCTTTTTATTTTGTATATCTGTATCAAAATCGATTTGATTAAAATCCGCTTTATTTTATCATCTATTCAAATGATTTTAGTGCGCTTATTTTACTATGGCATTATTGCCTAACCTGTTTGAGATATATTAATATTTGATGA  >  USA300TCH1516_ALE/2660467‑2660737

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.