New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	17 (0.890)	4 (0.240)	4/246	1.8	21.1%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	15 (0.890)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

TTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATA  >  USA300TCH1516_ALE/909603‑909866                                                                                                                                          |                                                                                                                               ttgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATCAATCAGCATGAAAGCATTACGGAGAGGGAGAGAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTCatta                                                                                                                             >  2:209189/1‑141 (MQ=255)        aaagtggaaaaaaaGGGAATAATTTTGAAACAAAGGGAAAGGGTATGAATAATAAATTATCTTGAAAATTTTATATATGCATATCTCCTGCTATTTTTATTGCCCTTGAACTTCCTTGATAATCTTGCTAATTATTCCTGc                                                                                                                      <  2:97401/134‑1 (MQ=255)                  aaaaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGCTTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATc                                                                                                            <  1:125328/141‑1 (MQ=255)                      gggCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaat                                                                                                        <  1:133038‑M2/141‑25 (MQ=255)                        gCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTa                                                                                                      >  2:168615/1‑141 (MQ=255)                             aTTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGc                                                                                                 >  2:186951/1‑141 (MQ=255)                             aTTTTGAAACAAAAGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGc                                                                                                 <  1:181825/141‑1 (MQ=255)                                       aaaGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGt                                                                                       >  1:68943/1‑141 (MQ=255)                                                    aTGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGc                                                                          <  1:168615/141‑1 (MQ=255)                                                       aataatAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCttt                                                                       >  1:187993/1‑141 (MQ=255)                                                           ataaATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTtttat                                                                   >  1:26712/1‑140 (MQ=255)                                                            taaATTATCTTGAAAATTGTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTtttaat                                                                  <  2:116308/141‑1 (MQ=255)                                                              aaTTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaactaacaataccctttaataacaacgattaaggggtta                                                                >  1:60725‑M2/1‑77 (MQ=255)                                                                     ttGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAgg                                                         <  2:187993/141‑1 (MQ=255)                                                                             tttATAAATGCATAGATAACAATGTTTTTATTGCCCTTGAACTTTCTTGATCATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTTATGTTGCTTGGCTTTTTAATTTAAACATGTATTtata                                                 <  2:171993/141‑1 (MQ=255)                                                                                      gCATATATAAGAATGTTTTGATTGCCCTATAACTTTCTTAATAATCTGGCTAATTCTTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTa                                        <  2:140809/141‑1 (MQ=255)                                                                                               aCAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATgagg                               >  1:13219/1‑140 (MQ=255)                                                                                                      tttgtttgCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaaaggggc                        >  1:64519‑M2/1‑37 (MQ=255)                                                                                                      tttGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTAtt                        <  1:64941/141‑1 (MQ=255)                                                                                                          aTTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACgg                    <  1:186951/141‑1 (MQ=255)                                                                                                                            tGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaaaggggcagtatatgcaaattatcgaatt  <  2:122390‑M2/141‑127 (MQ=255)                                                                                                                                          |                                                                                                                               TTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATA  >  USA300TCH1516_ALE/909603‑909866

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.