New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	559607 =	NA (NA)	3 (0.110) +A	3/268	4.2	9.7%	noncoding (651/2921 nt)	rrl2	23S ribosomal RNA
	?	CP000730	683996 =	28 (1.020)					coding (327/1047 nt)	USA300HOU_0628	hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAATTTTTAGCTCCCGCATTAAGACCATCTTCAATAGTTGGATATGTTGAATCATGAATCGATTTTGAACCCATAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTATCAATACCATTTGCCGAAACATTACCGC  >  CP000730/683862‑684135                                                                                                                                       |                                                                                                                                            aaaTTTTTAGCTCCCGCATTAAGACCATCTTCAATAGTTGGATATGTTGAATCATGAATCGATTTTGAACCCATAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCaata                                                                                                                                       >  2:101443/1‑141 (MQ=255)         aGCTCCCGCATTAAGACCATCTTCAATAGTTGGATATGTTGAATCATGAATCGATTTTGAACCCATAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCAt                                                                                                                               <  2:112177/141‑1 (MQ=255)           cTCCCGCATTAAGACCATCTTCAATAGTTGGATATGTTGAATCATGAATCGATTTTGAACCCATAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATaa                                                                                                                             <  2:173870/141‑1 (MQ=255)                                cAATAGTTGGATATGTTGAATCATGAATCGATTTTGAACCCATAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTAt                                                                                                        >  1:150723/1‑141 (MQ=255)                                    aGTTGGATATGTTGAATCATGAATCGATTTTGAACCCATAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTAttttt                                                                                                    >  1:95273/1‑141 (MQ=255)                                     gTTGGATATGTTGAATCATGAATCGATTTTGAACCCATAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTAtttttt                                                                                                   >  2:150337/1‑141 (MQ=255)                                                tGAATCATGAAGCGATTTCGAACCCCTACCATACAAAGGATTATTTTGTCTTGTCGCATTTTCACCTTTACCCCATTGTTATTCACTCGCAATAATGTCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAAtttt                                                                                        <  2:187644/141‑1 (MQ=255)                                                     cttaattCGATTTTAAACCCTTACCAGACAAAGATTTATTTTGTCTTGTCGCTTTTTTTCCTTTACCCCTTTTTGATTAATTGGAAATAAGGGCCATAAAAATATTCCCAGGTACTTTATTTTTTTCTGCAATTTTCTGTa                                                                                   <  1:14308/135‑1 (MQ=255)                                                                   gAACCCATAACAGACAAAGGATTATTTTGTCATGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCATAGGTACTTTATTTTTTTTTCCTATTTTCTGTATTTCTTTTCCTTTa                                                                     >  2:189448/1‑141 (MQ=255)                                                                        cATAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCctc                                                                <  2:19459/141‑1 (MQ=255)                                                                         aTAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCctct                                                               >  1:244711/1‑141 (MQ=255)                                                                              aGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCACTAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTTCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAAttt                                                          >  2:282125/1‑141 (MQ=255)                                                                              aGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAAttt                                                          >  1:225841/1‑141 (MQ=255)                                                                               gACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAAtttt                                                         >  2:158702/1‑141 (MQ=255)                                                                                 cAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTcc                                                       <  1:61631/141‑1 (MQ=255)                                                                                         tattTTGTCTTGTCGCATTTTCTCCTTTCCCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTAACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCCCTTTTAg                                               >  1:119745/1‑141 (MQ=255)                                                                                                  ttgtcGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGt                                      <  2:55242/141‑1 (MQ=255)                                                                                                    tttgctttttCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTa                                    >  2:205836/7‑141 (MQ=255)                                                                                                    gtcGCATTTACTCCTTAACCCCCTTGTGATTCACACGCAATAACGGCCATAAAAAGATTCACAGGTACTTTATTTTTTTCTGCTATCTTCTGTATGTCTTTTCCTTTACCCTTTATTTTTTCACCTTTATCTTTTTAGttt                                    >  2:245748/1‑140 (MQ=255)                                                                                                          ttttCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTa                              <  2:6230/141‑1 (MQ=255)                                                                                                          ttttCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTa                              <  2:248896/141‑1 (MQ=255)                                                                                                              ctcCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTATCaa                          >  2:252760/1‑141 (MQ=255)                                                                                                                           ttGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTATCAATACCATTTGCCGa             <  1:150337/141‑1 (MQ=255)                                                                                                                               tccttgcacGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTATCAATACCATTTGCCGAAACa         <  1:36515/133‑1 (MQ=255)                                                                                                                               gATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTTTTTTTTTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCTACCTTTAGCATTTTCGTTAAACTTATCAATACCATTTTCCGaaatt         >  2:109223/1‑139 (MQ=255)                                                                                                                                aTTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTATCAATACCATTTGCCGAAACAt        >  1:162404/1‑141 (MQ=255)                                                                                                                                   cACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCATTTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTATCATTTTCGTTAAACTTATCAATACCATTTCCCGAAACATTAc     >  1:31842/1‑141 (MQ=255)                                                                                                                                     cTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTATCAATACCATTTGCCGAAACATTACCg   <  2:95273/141‑1 (MQ=255)                                                                                                                                      tCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTATCAATACCATTTGCCGAAACATTACCGc  >  2:33489/1‑141 (MQ=255)                                                                                                                                       |                                                                                                                                            AAATTTTTAGCTCCCGCATTAAGACCATCTTCAATAGTTGGATATGTTGAATCATGAATCGATTTTGAACCCATAACAGACAAAGGATTATTTTGTCTTGTCGCATTTTCTCCTTTACCCCATTGTGATTCACTCGCAATAATGGCCATAAAAATATTCACAGGTACTTTATTTTTTTCTGCAATTTTCTGTATTTCTTTTCCTTTACCCTCTAATTTTCCACCTTTAGCATTTTCGTTAAACTTATCAATACCATTTGCCGAAACATTACCGC  >  CP000730/683862‑684135

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.