New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	10 (0.390)	6 (0.270)	6/226	NT	28.1%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	22 (1.000)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCG  >  USA300TCH1516_ALE/895645‑895906                                                                                                                                             |                                                                                                                          aaGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGt                                                                                                                           <  2:134886/141‑1 (MQ=255)     gttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaattatt                                                                                                                       <  1:10111‑M1/5‑1 (MQ=255)         tcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTg                                                                                                                   <  1:3551‑M1/9‑1 (MQ=255)           aagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCt                                                                                                                 <  1:237671‑M1/11‑1 (MQ=255)            agggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTa                                                                                                                >  2:131379‑M1/130‑141 (MQ=255)               aTCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAaat                                                                                                             <  1:90822/141‑1 (MQ=255)                          gcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCATTta                                                                                                  <  2:147605‑M1/26‑1 (MQ=255)                             taattttgaaacaaagtgcaagagtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgcttgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATtaaat                                                                                               >  2:9178‑M1/113‑141 (MQ=255)                               aaTTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAAAACAATGGTGCAGTTATTCCTGCTAAATAATACCCATtaaataa                                                                                             >  1:48985/1‑141 (MQ=255)                                          aagaatGACATAAAGAGTGTACGATAATTAAAGTATTAATTGGAGTATTAANATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTACTGCTAAATAATACCAATTAAATAACAATACCCttt                                                                                  <  2:5068/141‑1 (MQ=255)                                              agGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaata                                                                              >  1:200171/1‑141 (MQ=255)                                                  gggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATaacaa                                                                          <  1:145723‑M1/50‑1 (MQ=255)                                                        gatgatAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATAGTGAAGTTATTCCTTCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGAtaa                                                                    >  2:51090/1‑139 (MQ=255)                                                                gAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTa                                                            >  2:261867/1‑141 (MQ=255)                                                                                  tGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAGCGATTAAGGGGTTATTTTTGTGGTATTGaaaa                                          <  1:302639/141‑1 (MQ=255)                                                                                   taaatgattatataacaatgttttgattgcccttgaacttacttgataatctggctaaTTATTCCTGCGAAATAATACCAAGTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAAt                                         >  2:11430‑M1/59‑141 (MQ=255)                                                                                               acTAAAGATATGTAAGACGTCATTAATGAAAAATACAATGGTGCAGTTATTCTAGCTAAATAATACCAATTAAATAAAAATACCATTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGcac                             <  2:11310/140‑1 (MQ=255)                                                                                                 tAAAGATATTAAAGACTTCATAAATGAAAAATACAAAGGTGCAGTTATGCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaa                           <  2:187581/141‑1 (MQ=255)                                                                                                     gATATTCAAGACTACATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTGATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAgg                       <  2:93999/141‑1 (MQ=255)                                                                                                         ttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCCAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTTTGGTATTGAAAATAAAAAAGGGCACAAAAGAGGCa                   <  2:39775‑M1/105‑1 (MQ=255)                                                                                                                          tccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATACAAATACCCTTTAATAACAACGATTAAGGGGATATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAAGGGCTGTatatgcaaactaacg  <  2:131704‑M1/122‑7 (MQ=255)                                                                                                                                             |                                                                                                                          AAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCG  >  USA300TCH1516_ALE/895645‑895906

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.