New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	14 (0.680)	5 (0.280)	3/246	2.3	23.1%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	21 (1.160)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAAT  >  USA300TCH1516_ALE/895645‑895924                                                                                                                                             |                                                                                                                                            ggttgttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaat                                                                                                                                             >  1:210194‑M1/141‑141 (MQ=255) aaGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTATAGATATTCTAGACTTCATTAATGAAAAAGACAATGGTGCAGt                                                                                                                                             <  1:189508/141‑1 (MQ=255)      cGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTc                                                                                                                                        >  1:96561/1‑141 (MQ=255)          aGATAAGCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGc                                                                                                                                    <  1:227754/141‑1 (MQ=255)            aTAATCCTTATGCAAAATTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCACTTATTCCTGCTa                                                                                                                                  <  2:126600/141‑1 (MQ=255)                tCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAaata                                                                                                                              >  1:84579/1‑141 (MQ=255)                gaaagaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAaata                                                                                                                              >  1:54006‑M1/126‑141 (MQ=255)                              tAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaatc                                                                                                                >  2:166900/1‑140 (MQ=255)                                               ggACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaataa                                                                                               >  1:95889/1‑141 (MQ=255)                                                        gatgatAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACATCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTCATAACAACGATTa                                                                                      >  2:7133/1‑141 (MQ=255)                                                                     acAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAAGAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAttttt                                                                         <  2:220232/140‑1 (MQ=255)                                                                                                atAAATATATTAAATTCCTTATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGcaca                                              <  2:13177/140‑1 (MQ=255)                                                                                                   aaGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaaa                                           <  1:139043/141‑1 (MQ=255)                                                                                                          tgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATGAAGGGGTTATTTTTATAGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAg                                    <  2:137723‑M1/106‑1 (MQ=255)                                                                                                            attgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGTCACAAAAGGGGCAGta                                  <  1:155493‑M1/108‑1 (MQ=255)                                                                                                            attgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAACGGGCAGta                                  <  2:153540‑M1/108‑1 (MQ=255)                                                                                                              gACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGAGATTATTTTTGTGTTATTGAAAATAAAAAAAGGCACAAAAGGGGCAGtata                                >  2:217165/1‑141 (MQ=255)                                                                                                                                        gctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACaaaa      <  1:72218‑M1/136‑1 (MQ=255)                                                                                                                                        gctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACaaaa      <  1:207238‑M1/136‑1 (MQ=255)                                                                                                                                         gCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGAATAAGGGATTATTTTTGTGGTATTGAAAATAAAAAAGAGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACaaaaa     >  2:60817/1‑141 (MQ=255)                                                                                                                                            gTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAAt  >  1:21615/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                            AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAAT  >  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.