New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	693013 =	48 (0.880)	3 (0.060)	3/248	3.4	5.9%	intergenic (‑40/+135)	USA300HOU_0635/USA300HOU_0636	possible replication initiation protein/hypothetical protein
	?	CP000730	693128 =	52 (1.030)					intergenic (‑155/+20)	USA300HOU_0635/USA300HOU_0636	possible replication initiation protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCC  >  CP000730/692991‑693266                                                                                                                                          |                                                                                                                                           aTCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTaaa                                                                                                                                         >  1:326097/1‑141 (MQ=255)          cAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATa                                                                                                                                >  2:247298/1‑141 (MQ=255)           aaGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATAc                                                                                                                               >  1:257530/1‑141 (MQ=255)             gCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACta                                                                                                                             <  1:620343/141‑1 (MQ=255)                aTTTGATACATGACCGTTCTCGCTTTTTTATTTTTTTTTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTatat                                                                                                                          >  2:117174/1‑141 (MQ=255)                aTTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTatat                                                                                                                          <  2:7280/141‑1 (MQ=255)                aTTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTatat                                                                                                                          <  2:249848/141‑1 (MQ=255)                   tGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGtt                                                                                                                       >  1:151638/1‑141 (MQ=255)                    gATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTa                                                                                                                      >  1:103613/1‑141 (MQ=255)                       aCATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTCGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGCTacac                                                                                                                   >  2:69814/1‑141 (MQ=255)                            aCCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCaa                                                                                                              <  1:356764/141‑1 (MQ=255)                              cGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAata                                                                                                            >  1:483621/1‑141 (MQ=255)                                   tcGCTTTTTTAACGAGTATTTGTCGAAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACAATATGTTAAACATCAATATCGcc                                                                                                       >  2:566950/1‑141 (MQ=255)                                    cGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCa                                                                                                      <  2:275246/141‑1 (MQ=255)                                        tttttAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAatat                                                                                                  >  2:33566/1‑141 (MQ=255)                                         ttttAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAAtata                                                                                                 >  2:429219/1‑141 (MQ=255)                                            tAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAata                                                                                                            <  2:10623/127‑1 (MQ=255)                                            tAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAata                                                                                                            >  1:10623/1‑127 (MQ=255)                                            tAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAAt                                                                                              <  1:43007/141‑1 (MQ=255)                                              aCGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACta                                                                                                                             <  2:322391/108‑1 (MQ=255)                                              aCGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACta                                                                                                                             >  1:322391/1‑108 (MQ=255)                                              aCGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGGGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATAc                                                                                            >  1:148655/1‑141 (MQ=255)                                                    aTTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCtt                                                                                      >  2:636022/1‑141 (MQ=255)                                                    aTTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCtt                                                                                      <  2:278650/141‑1 (MQ=255)                                                    aTTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCtt                                                                                      <  2:307347/141‑1 (MQ=255)                                                    aTTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCtt                                                                                      <  2:477412/141‑1 (MQ=255)                                                     tttGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTc                                                                                     >  2:67688/1‑141 (MQ=255)                                                       tGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCa                                                                                   <  2:75495/141‑1 (MQ=255)                                                                   cGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTa                                                                       <  2:417105/141‑1 (MQ=255)                                                                         aaTGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTc                                                                 <  2:95365/141‑1 (MQ=255)                                                                          aTGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCt                                                                <  2:483621/141‑1 (MQ=255)                                                                             cTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAAt                                                                                         >  2:81480/1‑113 (MQ=255)                                                                             cTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAAt                                                                                         <  1:81480/113‑1 (MQ=255)                                                                             cTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGcc                                                             >  2:402845/1‑141 (MQ=255)                                                                               tAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCAt                                                           >  2:391906/1‑141 (MQ=255)                                                                                 aCGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGt                                                         <  2:215906/141‑1 (MQ=255)                                                                                 aCGCACTCCGTGCTTGCATTTCTGCACCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTTATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGt                                                         <  1:38515/141‑1 (MQ=255)                                                                                  cGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTc                                                        >  2:125772/1‑141 (MQ=255)                                                                                   gCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTcc                                                       >  2:517380/1‑141 (MQ=255)                                                                                     aCTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTg                                                     >  1:28539/1‑141 (MQ=255)                                                                                        ccGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCtt                                                  >  1:302404/1‑141 (MQ=255)                                                                                          gTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCa                                                <  2:326097/141‑1 (MQ=255)                                                                                           tGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCAc                                               >  2:527650/1‑141 (MQ=255)                                                                                            gCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACt                                              >  1:326232/1‑141 (MQ=255)                                                                                               tGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCaa                                           <  2:103613/141‑1 (MQ=255)                                                                                                gCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAg                                          <  2:557181/141‑1 (MQ=255)                                                                                                gCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAg                                          <  2:504525/141‑1 (MQ=255)                                                                                                      cTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATa                                    <  2:151638/141‑1 (MQ=255)                                                                                                                      tAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGt                    >  1:210939/1‑141 (MQ=255)                                                                                                                           gCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCg               <  1:117174/141‑1 (MQ=255)                                                                                                                           gCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCg               >  1:159494/1‑141 (MQ=255)                                                                                                                            cTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGt              <  1:247298/141‑1 (MQ=255)                                                                                                                                       tGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGc   >  1:480113/1‑141 (MQ=255)                                                                                                                                        gTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGcc  >  1:18507/1‑141 (MQ=255)                                                                                                                                        gTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGcc  >  1:445719/1‑141 (MQ=255)                                                                                                                                        gTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGcc  >  1:445721/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                           ATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAACATCAATATCGCCAATATAAATACAATCTTCCAAATTCACTTGTAGCATTCTGCCATGTCCTGCTTCACTCAAGCTCATACACAATAGACAAAGGTCAGCGTAAATTTTAGGCC  >  CP000730/692991‑693266

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