New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	29 (1.130)	8 (0.350)	7/246	1.6	27.9%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	16 (0.710)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

GTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCG  >  USA300TCH1516_ALE/909602‑909874                                                                                                                                           |                                                                                                                                       gttgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTAATCATCTTGCTAAtt                                                                                                                                      <  2:7110‑M2/141‑3 (MQ=255)  ttgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAtta                                                                                                                                     <  1:61752‑M2/141‑4 (MQ=255)   tgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttat                                                                                                                                    <  1:89100‑M2/141‑5 (MQ=255)       ttCCAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcct                                                                                                                                >  1:46000‑M2/1‑133 (MQ=255)       ttCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcct                                                                                                                                >  1:267062‑M2/1‑133 (MQ=255)             ggCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaa                                                                                                                          >  1:88578‑M2/1‑127 (MQ=255)               gagagagaGGGGATAGGTTTGAGAGGAAGGGATAGGGTATGAATAATAAATTATCTTTAAAATTTTATAAGTGTATGTATAACTATGTTTTGATTGCCATTGAACTTTCTTGATTATCTGGTTAATTATTCCTGTtatata                                                                                                                        <  2:129757/134‑1 (MQ=255)                            aaagTTTGAAAAAAAAGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTTATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaat                                                                                                           >  2:166912‑M2/2‑112 (MQ=255)                                   gAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGt                                                                                                    <  2:113969/141‑1 (MQ=255)                                                     aTGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGc                                                                                  <  2:218263/141‑1 (MQ=255)                                                      tGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCt                                                                                 >  1:195608/1‑141 (MQ=255)                                                      tGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTCAGTTGGCTAGATCCCCCCTAGAAGGAGGCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCt                                                                                 >  2:211596/1‑141 (MQ=255)                                                            ataaATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTTGGCTTtttaa                                                                           >  1:213935/1‑141 (MQ=255)                                                              aaaTTATATTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggtt                                                                         >  2:251177‑M2/1‑78 (MQ=255)                                                              aaaCTATCTTAAAAATTTTATAAAGGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAgtattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggtt                                                                         >  2:25781‑M2/1‑78 (MQ=255)                                                                 ttATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTtttaatttaa                                                                      >  1:87347/1‑141 (MQ=255)                                                                        gAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtgg                                                               >  2:54407‑M2/1‑68 (MQ=255)                                                                             ttttATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTtat                                                          >  1:22401/1‑141 (MQ=255)                                                                             ttttATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTtat                                                          >  2:25081/1‑141 (MQ=255)                                                                                 ataAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattaaaaa                                                      <  2:40701‑M2/141‑83 (MQ=255)                                                                                       gCATATATAATAATGTTTTGATTGCCCTTGAACTTCTTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTa                                                <  2:50959/141‑1 (MQ=255)                                                                                                     gTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGCTGTTGCTGGGCTTTTTAATTTAAACAGATCTTCATATGATCTTTAAGAATGAGATACTa                                  >  2:221260/1‑141 (MQ=255)                                                                                                     gTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATCAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGTTCTTTATATGCTATTTAGGAATGACATACTa                                  >  2:40967/1‑141 (MQ=255)                                                                                                        ttGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTACACAGATATTTATATGATATTTAGGAATGAGATGCTATTa                               >  2:187891/1‑141 (MQ=255)                                                                                                           aTTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATTATATTTAGGGATGAGATGCTATTACgg                            >  2:291814/1‑141 (MQ=255)                                                                                                                       cTTCATTGATAATCTGGCTAAttattcctgctaaataataccaattaaatcaaaataccctttaataagaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaaaggggcagtctatgcaaattat                <  1:289466‑M2/141‑121 (MQ=255)                                                                                                                          ccTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGACATTGAGGAATGAGATGCTATTACGGATAAAGTAAAATCCt             >  1:230446/1‑141 (MQ=255)                                                                                                                             tGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaaaggggcagtatatgcaaattatcgaatt          <  2:231907‑M2/141‑127 (MQ=255)                                                                                                                               aTAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCtatacg        <  2:213935/141‑3 (MQ=255)                                                                                                                                 aaTCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATatgca      >  2:166658/1‑141 (MQ=255)                                                                                                                                     tGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaaaggggcagtatatgcagattatcgaattttaaacaa  <  1:165813‑M2/141‑135 (MQ=255)                                                                                                                                           |                                                                                                                                       GTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCG  >  USA300TCH1516_ALE/909602‑909874

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ 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.