New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	30 (1.150)	9 (0.390)	9/246	1.3	27.1%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	22 (0.960)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAAT  >  USA300TCH1516_ALE/895645‑895924                                                                                                                                             |                                                                                                                                             aaGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGt                                                                                                                                              <  2:219012/141‑1 (MQ=255) aaGTACGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGTACATCAAAATACTCCATCACCCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGt                                                                                                                                              <  1:221984/141‑1 (MQ=255)   gTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑Ta                                                                                                                                           >  2:169230/1‑141 (MQ=255)     gttttcaagtgcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcacttgaacttccttgataatctggctaat‑tatt                                                                                                                                         >  1:202350‑M1/137‑141 (MQ=255)          aGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGc                                                                                                                                    <  1:66825/141‑1 (MQ=255)              ggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaT‑TATTCCTGCTaaa                                                                                                                                >  2:45126‑M1/128‑141 (MQ=255)                tCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACACTGCACAGACAGTCAAGACTTCATTAATGAACAATACAATGGTGCAGT‑TATTCCTGCTAaata                                                                                                                              >  1:70134/1‑141 (MQ=255)                 aaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaT‑TATTCCTGCTAaataa                                                                                                                             >  2:21952‑M1/125‑141 (MQ=255)                     aaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaT‑TATTTTTGCTAAATAATAcc                                                                                                                         <  1:112975‑M1/21‑1 (MQ=255)                     aTGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAACGAATACAATCTAAAGATATTCAAGACTTCATTAATAAAAAATACAATGGTTCAGT‑TATTCCTGCTAAATAATAcc                                                                                                                         >  2:93018/1‑141 (MQ=255)                     aTGAAAACTTAGTGGCTGTTAAAGAAGGACATCAAGATGATAAGAAAAGCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATAcc                                                                                                                         <  2:208335/141‑1 (MQ=255)                            cTTAATTGATGTTAAAGAATGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGGATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATtaaa                                                                                                                  <  2:34795/141‑1 (MQ=255)                              aattattaaacaaaaggcaaaggtatgaataataaattatgttgaaaattttataaatgcatatataacaatgtttttattgcccttgaacttacttgataatctggctaaT‑TATTCCTGCTAAATAATACCAATtaaata                                                                                                                >  2:140343‑M1/112‑141 (MQ=255)                                aTTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATAcc                                                                                                                         >  1:152598/1‑130 (MQ=255)                                aTTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATAcc                                                                                                                         <  2:152598/130‑1 (MQ=255)                                              gcaagggtattaataataaattatcttgaaaattgtataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctgtctaaT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaata                                                                                                >  2:194382‑M1/96‑141 (MQ=255)                                                gACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGGATTACAATCTAAAGATACGCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaataaa                                                                                              >  1:37957/1‑140 (MQ=255)                                                 agggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCTTTTAATaaca                                                                                             <  2:112913‑M1/49‑1 (MQ=255)                                                   aTCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATaacaac                                                                                           <  2:7704/141‑1 (MQ=255)                                                   aTCAAGATGATAAGAAAAGCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATaacaac                                                                                           >  2:233442/1‑141 (MQ=255)                                                         atgatAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTaa                                                                                     <  1:52611/141‑1 (MQ=255)                                                            atAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTAAATAATCAACTGAACAACAGACAAGTGTAGATCT‑CGGAATAATAACAATTAAATAAAAATACCCTTTAATAACAACGATTACggg                                                                                  >  2:65006/1‑141 (MQ=255)                                                               aGAAAATAAAAGAACTAATTTAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGtt                                                                               <  2:181082/141‑1 (MQ=255)                                                                 aaaaTCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAt                                                                             <  1:63185/141‑1 (MQ=255)                                                                         aGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAACATACAATGGAACAGC‑TACACCTGCTAAATAATACCAACTAAATAAACATCCCCCTTAATACCAACGATCAAAGCATTATTTTtgttc                                                                     >  2:35669/1‑139 (MQ=255)                                                                         aGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTgg                                                                     >  1:55754/1‑141 (MQ=255)                                                                                   aaaGTAATACAATCGAAAGATAATCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAAt                                                           <  2:286765/140‑1 (MQ=255)                                                                                                tgaaaGATATTCAAGACTTCATTAATGAAAAATACAGTGGTGAAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAAGACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGcaca                                              <  1:77278/139‑1 (MQ=255)                                                                                                  aaaGATATTAAATACTTCATTAATGAAAAATAAAATTGTTGAGT‑TAATACTGATAAATAATACAAATTAAATAAAAATACCCTTTAATAACAACTATTAAGGTGTTATTTTTATAGTATTAAAAATAAAAAAGGGCACaaa                                            <  2:18209/141‑1 (MQ=255)                                                                                                    aGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAg                                          <  1:257280/141‑1 (MQ=255)                                                                                                        atTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGc                                      >  1:182442/1‑141 (MQ=255)                                                                                                                   ttgaacttccttgataatctggctaaT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCaa                           >  1:6188‑M1/27‑141 (MQ=255)                                                                                                                   ctttAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCaa                           >  2:298045/3‑141 (MQ=255)                                                                                                                   cATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCaa                           >  1:292378/1‑141 (MQ=255)                                                                                                                     gaacttccttgataatctggctaaT‑TATTCCTACTAAATAATACCAATTAAATAAGAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGTGCACAAAAGGGGCAGTATATGCAAAt                         <  2:266582‑M1/117‑1 (MQ=255)                                                                                                                        cttccttgataatctggctaaT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACACTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTAt                      <  1:20702‑M1/120‑1 (MQ=255)                                                                                                                          tccttgataatctggctaaT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGAACAAAACGGCCAGTATATGCAAATTATCg                    <  1:169886‑M1/122‑1 (MQ=255)                                                                                                                          gAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCg                    >  1:203592/1‑141 (MQ=255)                                                                                                                              tgataatctggctaaT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAAtt                <  2:218343‑M1/126‑1 (MQ=255)                                                                                                                                 aCAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGATATTTTTGTGGTATTGAAAATAAAAAAGGGCAGAAAATGGGCAGTATATGCAAAATATAGAATTTTa             >  2:101836/1‑141 (MQ=255)                                                                                                                                     tGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACa         <  2:182442/141‑1 (MQ=255)                                                                                                                                            gT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAAt  >  1:106136/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                             AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGT‑TATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAAT  >  USA300TCH1516_ALE/895645‑895924

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