New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	25 (0.740)	5 (0.170)	5/226	NT	20.5%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	17 (0.580)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAA  >  USA300TCH1516_ALE/895645‑895923                                                                                                                                             |                                                                                                                                           ggttgttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaat                                                                                                                                            >  2:28470‑M1/141‑141 (MQ=255) aaGTGCCAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGt                                                                                                                                            <  1:100528/141‑1 (MQ=255)  aGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAAAGCTGCAGtt                                                                                                                                           >  2:65436/1‑141 (MQ=255)  aGTGCGAAAGATAATCCTGATGCAAACTTAATAGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATCAATGAAAACTACACTGGTGCAGtt                                                                                                                                           >  2:287671/1‑141 (MQ=255)   ttgttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaatta                                                                                                                                          <  1:147641‑M1/3‑1 (MQ=255)     gagAAAGATAATCCTTATGCAAAATTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTAtt                                                                                                                                        <  2:301240/139‑1 (MQ=255)          aaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGc                                                                                                                                   >  2:88151‑M1/132‑141 (MQ=255)                aaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttcctttataatctggctaaTTATTCCTGCTAaata                                                                                                                             >  2:336267‑M1/126‑141 (MQ=255)                        aaaaaTTAATTGCTGTTAAAGAATGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTAATACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAAt                                                                                                                     <  2:47649/140‑1 (MQ=255)                             ttAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAAGTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaat                                                                                                                <  1:10686/141‑1 (MQ=255)                              tAATTGATGTTAAAGAAGGACATCAAAATGATAAAAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaata                                                                                                               <  2:332103/141‑1 (MQ=255)                                  ttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctacTTCTTCATGCTCAATAATACCAATTAAATaaaaa                                                                                                           >  1:305079‑M1/108‑141 (MQ=255)                                    cTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACAAATTAAATaaaaaaa                                                                                                         >  2:58376/1‑139 (MQ=255)                                          aagaagGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCttt                                                                                                   <  1:282892/141‑1 (MQ=255)                                          aagaagGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCttt                                                                                                   <  2:401283/141‑1 (MQ=255)                                               ggACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaataa                                                                                              >  2:301889/1‑141 (MQ=255)                                               ggACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACAAATTAAATAAAAATACCCTTtaataa                                                                                              >  1:278499/1‑141 (MQ=255)                                                     cAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGa                                                                                        <  2:380171/141‑1 (MQ=255)                                                       aGATGATAAGAAAATCAAAGCATTAATTACAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATAGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGAtt                                                                                      <  2:345539/141‑1 (MQ=255)                                                              taaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGt                                                                               >  2:147641‑M1/80‑141 (MQ=255)                                                                         aGCATTAATTGAAGTATTACAACCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTgg                                                                    <  2:271406/141‑1 (MQ=255)                                                                           aaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTa                                                                  <  1:252320‑M1/75‑1 (MQ=255)                                                                            atgaaTTGAAGTATTAGAATCTAAAGAAATTCAAGACTTCAATAATGAAAAATACAATGGTACAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTAt                                                                 <  2:95406/138‑1 (MQ=255)                                                                             attttataaatgcatatataacaatgttttgattgcccttgaacttccttgatactctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTAtt                                                                <  1:44372‑M1/77‑1 (MQ=255)                                                                                aTTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaa                                                             <  1:254814/141‑1 (MQ=255)                                                                                 ttGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATCACAACGATTAAGGGGTTATTTTTGTGGTATTGaaa                                                            >  1:35829/1‑141 (MQ=255)                                                                                   gAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAAt                                                          <  1:104281/141‑1 (MQ=255)                                                                                         ttACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATaaaaaa                                                    >  2:152407/1‑141 (MQ=255)                                                                                             aaTCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGc                                                <  1:324041/141‑1 (MQ=255)                                                                                                    aGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAACAAAGGGCACAAAAg                                         >  2:244559/1‑141 (MQ=255)                                                                                                      atatTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAggg                                       >  1:327412/1‑141 (MQ=255)                                                                                                       tatTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAgggg                                      <  1:12558/141‑1 (MQ=255)                                                                                                       aatTCAAGACTTAATTAATGAAAAATACAGTGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAgggg                                      <  2:345397/140‑1 (MQ=255)                                                                                                           cAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGt                                  >  1:14896/1‑141 (MQ=255)                                                                                                            aaGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGta                                 >  1:356724/1‑141 (MQ=255)                                                                                                                        cttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTGTTGCAAATAAAAAGGGGCACAAAAGGGGCAGTATATGCAAATTAt                     <  1:112524‑M1/120‑1 (MQ=255)                                                                                                                          aaaaaaGAAAATGGAGCAGTAATGCATGCAAAATAAAAACAATAAAATAAAAAAACTTATAAATAAAAACAAGAAAGGGGTTATTTTTATGGTAATGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCg                   <  2:198746/140‑1 (MQ=255)                                                                                                                                    aTGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTaaaa         >  1:359074/1‑140 (MQ=255)                                                                                                                                           aGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTCTCGAATTTTAAACaaaaaaa  >  2:347134/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                           AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAA  >  USA300TCH1516_ALE/895645‑895923

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.