New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2687471 =	58 (1.540)	3 (0.090)	3/256	5.8	5.4%	intergenic (+25/+44)	clp/USA300HOU_2543	S14 family endopeptidase Clp/hypothetical protein
	?	CP000730	2687511 =	52 (1.500)					intergenic (+65/+4)	clp/USA300HOU_2543	S14 family endopeptidase Clp/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TTTAGATCATACAGACGTTAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAATTTTACTAGTGTATATAAGGCATATCC  >  CP000730/2687374‑2687643                                                                                                                                          |                                                                                                                                     tttAGAGCATACAGACGTTAAACATGTGGATATCGATGGTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCAtttttttca                                                                                                                                   <  2:63896/141‑3 (MQ=255)  ttAGATCATACAGACGTTAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAat                                                                                                                                  <  1:162355/141‑1 (MQ=255)   tAGATCATACAGACGTTAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAatt                                                                                                                                 >  2:181364/1‑141 (MQ=255)        cATACAGACGTTAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTc                                                                                                                            <  1:240528/141‑1 (MQ=255)        cATACAGACGTTAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTc                                                                                                                            >  1:47460/1‑141 (MQ=255)          tACAGACGTTAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTccc                                                                                                                          >  2:133797/1‑141 (MQ=255)          tACAGACGTTAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTccc                                                                                                                          >  1:308408/1‑141 (MQ=255)                 gTTAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGaaaa                                                                                                                   <  1:248748/141‑1 (MQ=255)                  ttAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAAt                                                                                                                  >  1:180025/1‑141 (MQ=255)                   tAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATg                                                                                                                 >  1:371111/1‑141 (MQ=255)                    aaaCATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGa                                                                                                                <  1:114227/141‑1 (MQ=255)                        aTGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCg                                                                                                            <  2:372864/141‑1 (MQ=255)                               tataGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCtgtgtg                                                                                                     <  1:189732/141‑1 (MQ=255)                                ataGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGc                                                                                                    <  2:226492/141‑1 (MQ=255)                                 taGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGct                                                                                                   >  1:183547/1‑141 (MQ=255)                                 taGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGct                                                                                                   >  1:129011/1‑141 (MQ=255)                                   gATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGctgt                                                                                                 <  2:16321/141‑1 (MQ=255)                                    aTGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGctgtt                                                                                                <  2:61455/141‑1 (MQ=255)                                       ttGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGctgttctg                                                                                             >  2:190998/1‑141 (MQ=255)                                         gAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGctgttctgtt                                                                                           >  2:113570/1‑141 (MQ=255)                                          aGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCtgttctgttc                                                                                          >  1:389194/1‑141 (MQ=255)                                           ggATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCAGCAAAAATTAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTcc                                                                                         <  1:130386/141‑1 (MQ=255)                                              tAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCcaca                                                                                      >  2:398151/1‑141 (MQ=255)                                               aaCGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCacaa                                                                                     <  1:18099/141‑1 (MQ=255)                                                    aTTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATc                                                                                <  1:8536/141‑1 (MQ=255)                                                    aTTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATc                                                                                <  2:123962/141‑1 (MQ=255)                                                       aGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACg                                                                             >  1:311112/1‑141 (MQ=255)                                                        gTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGa                                                                            >  1:410689/1‑141 (MQ=255)                                                          cGTACAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGAtt                                                                          <  1:38499/141‑1 (MQ=255)                                                             tatttaccttttaCGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAAt                                                                       >  1:145569/13‑141 (MQ=255)                                                                    aaaTAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACAt                                                                >  2:187790/1‑141 (MQ=255)                                                                       tAACGACACTTTAACATATCGCGAATCAAAAATGACCATCAGGTCGCCCTTGCCTGTGCTCATGTTTTTAATTATTTCGCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTa                                                             >  2:354614/1‑141 (MQ=255)                                                                            acacTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGACGGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTTTTCTGTTCCACAACACTCACGATTAATGTCACATGTACgaca                                                        >  1:393627/1‑141 (MQ=255)                                                                              acTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACAtt                                                      <  1:126893/141‑1 (MQ=255)                                                                                       tatCGCGCATCAAAAATGAGCATCAGGGCGCCCTTGCCTGTGCTCATTTTTTGAATTATTGCCCTGGAAAAGGATTCGCTTTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGtt                                             >  1:378072/1‑141 (MQ=255)                                                                                        atCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGttt                                            <  1:166209/141‑1 (MQ=255)                                                                                         tCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGtttt                                           >  1:58118/1‑141 (MQ=255)                                                                                         tCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGtttt                                           >  1:417471/1‑141 (MQ=255)                                                                                         tCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGtttt                                           >  2:64550/1‑141 (MQ=255)                                                                                            cgcATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGaa                                        >  2:233067/1‑141 (MQ=255)                                                                                              cATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAGTGTCACATGTACCACATTTTCCTTGTTTTGAACg                                      <  1:309057/141‑1 (MQ=255)                                                                                               aTCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGATCATTTTTTTAATAATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACAACATTTTCCTTGTTTTGAACGc                                     >  1:146868/1‑141 (MQ=255)                                                                                                 cAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACTATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCtt                                   <  2:153897/141‑1 (MQ=255)                                                                                                     aaTGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGaaa                               >  2:233048/1‑141 (MQ=255)                                                                                                        gAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAAt                            <  2:310693/141‑1 (MQ=255)                                                                                                        gAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAAt                            <  2:311112/141‑1 (MQ=255)                                                                                                        caacaccatgTCGCACTTGCCCGATCTCACTTTCTTAATTATTTCCCTGTCAAATGGTTCGCTGTGTTCTGTTCTGTTCTACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAAt                            >  2:285390/10‑141 (MQ=255)                                                                                                          gCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAAttt                          >  1:242514/1‑141 (MQ=255)                                                                                                            aTCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTCTTTCCCTGGAAAATGTTTCTCTTTGTGCTGTTCTGTTCCACAACAATCACGATTAATGCCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAATTTTa                        >  2:275995/1‑141 (MQ=255)                                                                                                               aGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAATTTTACTa                     <  2:20978/141‑1 (MQ=255)                                                                                                                   cgccattcacTGTGCTCATTTTTTTAATTATTTACAAAGAAAATAATTCGATGTGTGGTGTTCTGTTACACAACACTAATGATTAATGTTACATATACCACATTTACCTTGTTTTGAACGCTTGAAAAATTTTACTAgtgt                 <  2:83110/132‑1 (MQ=255)                                                                                                                   cGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAATTTTACTAgtgt                 <  2:180025/141‑1 (MQ=255)                                                                                                                                  tCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAATTTTACTAGTGTATATAAGGCATATcc  <  1:362038/141‑1 (MQ=255)                                                                                                                                          |                                                                                                                                     TTTAGATCATACAGACGTTAAACATGTGGATATAGATGTTGAGGATAACGAATTAGTCGTAAAAGGTAAATAACGACACTTTAACATATCGCGCATCAAAAATGAGCATCAGGTCGCCCTTGCCTGTGCTCATTTTTTTAATTATTTCCCTGGAAAATGATTCGCTGTGTGCTGTTCTGTTCCACAACAATCACGATTAATGTCACATGTACCACATTTTCCTTGTTTTGAACGCTTGAAAAATTTTACTAGTGTATATAAGGCATATCC  >  CP000730/2687374‑2687643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.