New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	36 (1.180)	19 (0.710)	15/246	0.6	36.0%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	36 (1.350)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAA  >  USA300TCH1516_ALE/895645‑895920                                                                                                                                             |                                                                                                                                        aaatGCGAAAGATAAACGTTAGACAAAGGTAATTGGTGTTAAAGAAGTACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCAGTAATGAAAAATACAATGGTGCAGt                                                                                                                                         <  2:140780/138‑1 (MQ=255) aaGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAAATGATAAAAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATAAAAACTACAATAGTGCAGt                                                                                                                                         >  1:148536/1‑141 (MQ=255)   ttgttttcacgggcaaaaaaagggcataattttgacacaacgacctggggtatgaataataaattatcttgaaaattttataaatgcatatataacaatattttgattgcccttgaacttccttcataatctggctaatta                                                                                                                                       <  2:161784‑M1/3‑1 (MQ=255)   ttgttttcaagggcaaaaaaagggcataattttgaattaatgggcaagtgtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgatttcccttgaacttccttgctaatcttgctaattt                                                                                                                                       <  2:162538‑M1/3‑2 (MQ=255)   ttgttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaatta                                                                                                                                       <  2:243052‑M1/3‑1 (MQ=255)     gCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAAGCGTAAATTTGATTGAGGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAACATACAATGGTGCAGTTAtt                                                                                                                                     >  2:266751/1‑141 (MQ=255)      cGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAACATACAATGGTGCAGTTATTc                                                                                                                                    >  2:260770/1‑141 (MQ=255)      cGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTAtca                                                                                                                                    >  2:156555/1‑139 (MQ=255)         aaGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTg                                                                                                                                 <  1:73974/141‑1 (MQ=255)           aagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaagtagcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCt                                                                                                                               <  2:176145‑M1/11‑1 (MQ=255)            cggggaaacaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTa                                                                                                                              <  1:280235‑M1/12‑1 (MQ=255)             tAATCCTTATGCAAACTTAATTGCAGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTaa                                                                                                                             <  2:184900/141‑1 (MQ=255)               gcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAaat                                                                                                                           >  1:346059‑M1/127‑141 (MQ=255)               gcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAaat                                                                                                                           >  1:347070‑M1/127‑141 (MQ=255)               aTCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAaat                                                                                                                           <  1:327777/141‑1 (MQ=255)                    tATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATAc                                                                                                                      <  1:193521/141‑1 (MQ=255)                       agggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTACATAATACcat                                                                                                                   <  1:283978‑M1/23‑2 (MQ=255)                        gggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaaattacttaataatctgtctaaTTATTCTTGCTAAATAatacccat                                                                                                                  <  2:282723‑M1/24‑4 (MQ=255)                            catAATTGCTATTAAAGAAGGACATCAAGATTATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaa                                                                                                              <  2:303977/139‑1 (MQ=255)                            attAATTGCTGTTAAAGTATGACATCAAGATGATAAGAAAATAAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaa                                                                                                              <  2:191173/140‑1 (MQ=255)                             ttAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaat                                                                                                             <  2:206743/141‑1 (MQ=255)                              tAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaata                                                                                                            >  1:304877/1‑141 (MQ=255)                               attttgaaacaaatgtcaagggtatgaataataaattttctttgaaatcttataaatgcatatataacaatgttttgattgccctcgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATtaaataa                                                                                                           >  2:342763‑M1/111‑141 (MQ=255)                                ttttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATtaaataaa                                                                                                          >  1:38116‑M1/110‑141 (MQ=255)                                         aaagtgcaagagtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttgtgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCtt                                                                                                 >  2:143907‑M1/101‑141 (MQ=255)                                         aaaGAAGGACATCAAGATGATAAGAAAATCTAATCATTATCTGCTCCGATCTGGTCTAAATATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCtt                                                                                                 <  1:349449/141‑1 (MQ=255)                                            gaagGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATCATACCAATTAAATAAAAATACCCTTtaa                                                                                              >  2:137188/1‑141 (MQ=255)                                                  cATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGGAGGAAATCCAGACAAATAATACTGATTAAATAAAAATACCGTTTAATaacaa                                                                                        >  1:81021/1‑141 (MQ=255)                                                  cATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTAAAGACTTCATTAATGAAAAATACAATAATGAAATTCTTCCATCTAAATAATACCAATTAAATAAAAATACACTTTAATaacaa                                                                                        >  2:159163/1‑141 (MQ=255)                                                    tCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACg                                                                                      >  2:251349/1‑141 (MQ=255)                                                       aGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCATGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGAtt                                                                                   >  2:263788/1‑141 (MQ=255)                                                                         gaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTgg                                                                 >  1:181763‑M1/69‑141 (MQ=255)                                                                         aGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTgg                                                                 >  1:12530/1‑141 (MQ=255)                                                                            aTTAATTGAAGTATTACAATCTAAAGATATTAAAGATTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTAt                                                              <  2:26523/141‑1 (MQ=255)                                                                                aTTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaa                                                          <  1:342135/141‑1 (MQ=255)                                                                                aTTGAAGTATTACAAAATAAAGATAGTCAAGACTTCAATAATAAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaa                                                          <  2:244958/141‑1 (MQ=255)                                                                                aTTAAAATATTAGAATCTAAAGCTATACAAGACTTAATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaa                                                          <  2:322994/141‑1 (MQ=255)                                                                                  agcaGTATCCCATTCTACAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaaaa                                                        <  1:180811/138‑1 (MQ=255)                                                                                  agaagttcagatataacaatgttttgattgtccttgaaatttcttaataatcttgataaTTATTCCTGCTAAATAATACCAATTAAATAATAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaaaa                                                        >  2:134949‑M1/60‑141 (MQ=255)                                                                                  aaaaaagcatatataacaatgttttgattgcccttgaacttccttaataatctggctaaTTATTCCTACTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaaaa                                                        >  2:208808‑M1/60‑141 (MQ=255)                                                                                          atatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAg                                                >  2:279454‑M1/52‑141 (MQ=255)                                                                                           tatataacaatgttttgattgcatttgaacttgattgataatctggataaTTAGTCCTGCTAAATAATTCCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGCATTGTTGATGTGTTATTTAAAATAAAAAAgg                                               >  2:198632‑M1/51‑141 (MQ=255)                                                                                               taacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCACTCAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGCTATTGAAAATAAAAAACGGcac                                           <  2:41683‑M1/95‑1 (MQ=255)                                                                                               taacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGCGGATATTTTTGTGCTATTGATAATCaaaaagcgtcc                                           <  2:313345‑M1/95‑6 (MQ=255)                                                                                                 acaatgttttgattgcccttgaacttccgtgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaa                                         >  1:149549‑M1/45‑141 (MQ=255)                                                                                                  caatgttttgattgcccttgaactaccttcataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaa                                        >  1:335942‑M1/44‑141 (MQ=255)                                                                                                       tatTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACACAAgggg                                   >  1:147084/1‑141 (MQ=255)                                                                                                       tatTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAgggg                                   >  1:107405/1‑141 (MQ=255)                                                                                                          tCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACACTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAg                                >  2:75611/1‑141 (MQ=255)                                                                                                              tgcccttgaccttccttgataatctggctaaTTATTCCTGCTAAATAATACCCATTAAATCAAAATACGCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAACTAAAAAAGGGCACAAAAGGGGCAGtata                            <  1:345829‑M1/110‑1 (MQ=255)                                                                                                              tgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGtata                            <  1:179319‑M1/110‑1 (MQ=255)                                                                                                              tgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGtata                            <  1:160021‑M1/110‑1 (MQ=255)                                                                                                              gACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTATGTGATATTGAAAATAACAAAGAGCAGAAAAGAGGCAGtata                            >  2:230012/1‑141 (MQ=255)                                                                                                               gcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTatat                           <  1:203456‑M1/111‑1 (MQ=255)                                                                                                                   cATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCaa                       >  1:74546/1‑141 (MQ=255)                                                                                                                   cATTAATGAAAAATACAATGGTGCAGTTATGCCTGCTAAATAATACAAATTAAATAAAAATACCCTTTAATAACAACGATGAAGGGGTTATTTATGGGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGGaa                       >  1:74612/1‑141 (MQ=255)                                                                                                                          gAAAAATACAATGGTGCAGTTATTCGTGCTCAATAATAGCAAGTAAATAAAAATACTATTTAAGAACAGAGATGAAGGGGATATTTTTGTGGTATTGAAAATAAAAAGGGGCACAACAAGGGCTGTTTAGGCAAATTATCg                >  2:21312/1‑141 (MQ=255)                                                                                                                          gAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATCGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCg                >  1:208579/1‑141 (MQ=255)                                                                                                                                  cAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTaa        >  2:120705/1‑141 (MQ=255)                                                                                                                                  cAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTaa        >  1:311238/1‑141 (MQ=255)                                                                                                                                     tgatGCATTTATGCATGCCAAAAAATAGACATAAAATAAAAATACCCTTTAATAATAACGATTAAGGGGTTATTTTTGTGGTGTTGAAAATAAAAAAGGGGACAAAAGGTGCAGTATATGCAAATTATCGAAGTTTAAACa     <  2:148536/138‑1 (MQ=255)                                                                                                                                        gctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACaaaa  <  2:56101‑M1/136‑1 (MQ=255)                                                                                                                                             |                                                                                                                                        AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAA  >  USA300TCH1516_ALE/895645‑895920

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.