New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	46 (1.140)	4 (0.110)	4/226	NT	11.3%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	23 (0.650)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

AGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTA  >  USA300TCH1516_ALE/895646‑895913                                                                                                                                            |                                                                                                                                 gttgttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaatt                                                                                                                                 <  1:473646‑M1/2‑1 (MQ=255) gttgttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaatt                                                                                                                                 <  1:242871‑M1/2‑1 (MQ=255) aGTGCGAAAGATAATCCTTATGCAAACGTAATTGATGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGtt                                                                                                                                 >  1:73554/1‑141 (MQ=255)         aGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGc                                                                                                                         <  2:94722/141‑1 (MQ=255)         aGATAATCCTTATGCAAACGTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGc                                                                                                                         <  2:376657/141‑1 (MQ=255)          aaaataaaaaaaagggcataattttgaaacaaaggtcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttcctttataatctggctaaTTATTCCTGCt                                                                                                                        >  2:25169‑M1/131‑141 (MQ=255)          aaaaaaaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCt                                                                                                                        >  2:190492‑M1/131‑141 (MQ=255)               tCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAaata                                                                                                                   >  1:368215/1‑141 (MQ=255)               tCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAaata                                                                                                                   <  1:354982/141‑1 (MQ=255)                    aaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataagtgcatatataacaatgatttgattgcgcttgaacttccttgataatctggctaaTTATTCCTgctaaataactca                                                                                                              <  2:429399‑M1/21‑5 (MQ=255)                          aCTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaa                                                                                                        <  1:31529/141‑1 (MQ=255)                           attAATTGCTGTTAAATAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaa                                                                                                       <  2:307658/140‑1 (MQ=255)                             tAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaata                                                                                                     <  1:238948/141‑1 (MQ=255)                             tAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAAACATCAACACTGATAACTACAACCCAGCAGCTACTCCTGCTAAATAATACCAATtaaata                                                                                                     >  1:188895/1‑141 (MQ=255)                                        aaaGAAGGACATTAAGATAATAAGAAAATCAAAGCATTAATTTAAGTATTAAAATCTAAAGATAATCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCtt                                                                                          <  2:92448/141‑1 (MQ=255)                                        aaaGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCtt                                                                                          <  1:253889/141‑1 (MQ=255)                                        aaaGAAGGACATCAAGATGATAAGAAAATCAAAGCAGTAAGTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTACTCCTGCTAAATAATACCAATTAAATAAAAATACCCtt                                                                                          <  1:256630/141‑1 (MQ=255)                                            aagGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaat                                                                                      <  1:203990/141‑1 (MQ=255)                                             agGACATCAAGATGATAAGAACAACCTCGGAATAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaata                                                                                     <  2:79757/141‑1 (MQ=255)                                              ggACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaataa                                                                                    <  1:485038/141‑1 (MQ=255)                                              ggACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaataa                                                                                    <  1:220888/141‑1 (MQ=255)                                                   tCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACg                                                                               >  1:222758/1‑141 (MQ=255)                                                   tCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACg                                                                               >  1:222704/1‑141 (MQ=255)                                                    cAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGa                                                                              >  1:32758/1‑141 (MQ=255)                                                             aaGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGt                                                                     <  2:96115/141‑1 (MQ=255)                                                             aaGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGt                                                                     <  1:432401/141‑1 (MQ=255)                                                             aaGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGt                                                                     <  1:265498/141‑1 (MQ=255)                                                                aaaaTCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAt                                                                  >  2:111730/1‑141 (MQ=255)                                                                 aaaaCAAAGCAGTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAtt                                                                 <  2:218638/141‑1 (MQ=255)                                                                  aaTCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAttt                                                                <  1:275790/141‑1 (MQ=255)                                                                   aTCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAtttt                                                               >  1:269858/1‑141 (MQ=255)                                                                    tCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAttttt                                                              <  2:368215/141‑1 (MQ=255)                                                                        aGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTgg                                                          >  1:78068/1‑141 (MQ=255)                                                                             tAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGATATTTTTGTGGCATTg                                                     >  2:227697/1‑141 (MQ=255)                                                                               aTTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaa                                                   >  2:152157/1‑141 (MQ=255)                                                                                 tGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaaaa                                                 <  1:399707/141‑1 (MQ=255)                                                                                  gAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAAt                                                >  2:193143/1‑141 (MQ=255)                                                                                    aGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAACACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACTCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATaa                                              >  2:153671/1‑141 (MQ=255)                                                                                     atgcatatataacaatgttttgattgcccttgtacttccttgataatctggctaaTTATTCCTGATAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATaaa                                             >  2:13449‑M1/56‑141 (MQ=255)                                                                                            aaTCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGc                                      >  1:454453/1‑141 (MQ=255)                                                                                              taacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGACTATTTTTGTGGTATTGAAAATAAAAAAGGGcac                                    <  2:94957‑M1/95‑1 (MQ=255)                                                                                                aaaaGATATTCAAGACTTCATTAAAGAAAAATACAATGGTGCAGTTATTCCTGATAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaa                                  <  2:252770/140‑1 (MQ=255)                                                                                                aaaaGATAATCAAGACTTAATTAATGAAAAATAAAAAGGTGCAGTTATTCATGCTAAAAAATAACAATTAAATAAAAATACACTTTAATAACAACGATTAAGGGGTTATTTTTGTAGTATTGAAAATAAAAAAGGGCACaa                                  <  2:209870/140‑1 (MQ=255)                                                                                                 aaaGATATTCAAAACTTAATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACACTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaa                                 <  2:141323/141‑1 (MQ=255)                                                                                                 aaaGATATTAAAGAATTCATGAATGAAAAATACAATGGTGAAGTTATTACTGATAAAAAATACCAATTAAATAAAAAGACCCATTAATAACAACGAGTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaa                                 <  2:417899/141‑1 (MQ=255)                                                                                                   aaatatTCAAGACTTCATTAATAAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAg                               <  1:329082/139‑1 (MQ=255)                                                                                                   aGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAg                               <  1:152157/141‑1 (MQ=255)                                                                                                   aGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAg                               <  1:128217/141‑1 (MQ=255)                                                                                                        ttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTCAATAAAAATACACTTTAATAACAACGATTAAGGGTTTATTTTTGTGGTATTGAAAATAAAAAAGAGCAcaaaagttgca                          <  2:129128‑M1/105‑6 (MQ=255)                                                                                                          gattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGATCACAAAAGGGGCAGt                        <  1:183248‑M1/107‑1 (MQ=255)                                                                                                           aaGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGta                       >  1:298905/1‑141 (MQ=255)                                                                                                                    ttAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTCTATGCcaaa              >  2:52533/1‑140 (MQ=255)                                                                                                                           aaaaTACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGaa       >  1:299951/1‑141 (MQ=255)                                                                                                                            aaaTACAATGGTGCAGTTATTCCTGCTAATTAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAAt      >  1:273513/1‑141 (MQ=255)                                                                                                                                aCAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTa  >  1:199868/1‑141 (MQ=255)                                                                                                                                aCAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTa  >  1:448705/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                 AGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTA  >  USA300TCH1516_ALE/895646‑895913

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