New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1114106	67 (1.010)	3 (0.050)	3/232	8.4	5.1%	intergenic (+35/‑4)	USA300HOU_1045/USA300HOU_1046	hypothetical membrane protein/hypothetical protein
	?	CP000730	= 1114131	54 (0.930)					coding (22/105 nt)	USA300HOU_1046	hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GTGATGATTATGTTGATTTCTAAAAAAGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTTTATTATAGAAAGGTCC  >  CP000730/1113997‑1114266                                                                                                                                       |                                                                                                                                        gTGATGATTATGTTGATTTCTAAAAAAGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACAtt                                                                                                                                   >  1:177986/1‑141 (MQ=255) gTGATGATTATGTTGATTTCTAAAAAAGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACAtt                                                                                                                                   >  1:318491/1‑141 (MQ=255)    atgatTATGTTGATTTCTAAAAAAGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTa                                                                                                                                >  2:38996/1‑141 (MQ=255)    atgatTATGTTGATTTCTAAAAAAGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTa                                                                                                                                >  2:299985/1‑141 (MQ=255)                 tttCTAAAAAAGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTAtttt                                                                                                                   >  1:422336/1‑141 (MQ=255)                      aaaaaaGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACt                                                                                                              >  2:755883/1‑141 (MQ=255)                        aaaaGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACttt                                                                                                            >  2:143635/1‑141 (MQ=255)                        aaaaGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACttt                                                                                                            >  2:713344/1‑141 (MQ=255)                              aTCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGtt                                                                                                      >  2:382304/1‑141 (MQ=255)                                 aaaaGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCtt                                                                                                   >  1:215598/1‑141 (MQ=255)                                  aaaGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTg                                                                                                  <  1:44649/141‑1 (MQ=255)                                         caacaCATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGtt                                                                                           >  1:513481/1‑141 (MQ=255)                                           acacATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTg                                                                                         >  1:263993/1‑141 (MQ=255)                                           acacATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTg                                                                                         >  1:263999/1‑141 (MQ=255)                                            cacaTAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGa                                                                                        <  1:299985/141‑1 (MQ=255)                                             acaTAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGaa                                                                                       <  2:114082/141‑1 (MQ=255)                                                  aGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTATAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTCTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGAtt                                                                                  >  2:66315/1‑141 (MQ=255)                                                  aGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGAtt                                                                                  >  1:37547/1‑141 (MQ=255)                                                   ggACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTa                                                                                 >  1:417034/1‑141 (MQ=255)                                                   ggACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTa                                                                                 >  1:562651/1‑141 (MQ=255)                                                   ggACGATGAGTATATTAATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTATTTCAATGTTAGAACGAttt                                                                                 >  2:305178/1‑140 (MQ=255)                                                     aCGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTaaa                                                                               >  1:788868/1‑141 (MQ=255)                                                      cGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAAt                                                                              <  1:38996/141‑1 (MQ=255)                                                            gTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACAt                                                                        <  2:303400/141‑1 (MQ=255)                                                              atatTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACAttt                                                                      <  2:449106/141‑1 (MQ=255)                                                                atTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTaa                                                                    >  2:511732/1‑141 (MQ=255)                                                                  ttATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTaaaa                                                                  <  1:522628/141‑1 (MQ=255)                                                                       aTTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACtt                                                             >  1:191309/1‑141 (MQ=255)                                                                         tAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAg                                                           <  1:34776/141‑1 (MQ=255)                                                                              tGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGaataa                                                      >  2:43730/1‑141 (MQ=255)                                                                              tGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGaataa                                                      >  2:222289/1‑141 (MQ=255)                                                                                    tAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAAtaataataa                                                >  1:656479/1‑141 (MQ=255)                                                                                       cAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAgtg                                             <  1:693903/141‑1 (MQ=255)                                                                                        aaaaGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAgtgt                                            >  2:577105/1‑141 (MQ=255)                                                                                         aaaGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTc                                           >  2:420897/1‑141 (MQ=255)                                                                                          aaGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTcc                                          >  1:138978/1‑141 (MQ=255)                                                                                            gAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGAtt                                                                                  <  2:726068/99‑1 (MQ=255)                                                                                            gAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGAtt                                                                                  >  1:726068/1‑99 (MQ=255)                                                                                            aaaaaaCCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCAt                                        <  2:360981/140‑1 (MQ=255)                                                                                                aaCCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTATAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGaaa                                    >  1:129165/1‑141 (MQ=255)                                                                                                 aCCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAAt                                   >  1:669642/1‑141 (MQ=255)                                                                                                 aCCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGGTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAAt                                   >  1:669621/1‑141 (MQ=255)                                                                                                      tAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGatat                              >  1:735850/1‑141 (MQ=255)                                                                                                       aaaaTGTTAAGTTGTTAATTATGAGATACAACCAACAATTTGATGGTGTGAGTTGTAACTTTGTAGTTCGTGGAATGGTTGAACGATTAAATAGACATTTAAAATACTTAGNATAATAATAAGTNTCCATGAAATGATAtt                             <  1:472544/141‑1 (MQ=255)                                                                                                         aaTGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTaaa                                                                   >  2:192037/1‑101 (MQ=255)                                                                                                         aaTGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTaaa                                                                   <  1:192037/101‑1 (MQ=255)                                                                                                           tGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAAcc                         <  2:215598/141‑1 (MQ=255)                                                                                                            gTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAAccc                        >  2:769493/1‑141 (MQ=255)                                                                                                              tAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCAt                      >  2:577439/1‑141 (MQ=255)                                                                                                                aGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGt                    <  1:511732/141‑1 (MQ=255)                                                                                                                    gttAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTtta                >  2:298192/1‑141 (MQ=255)                                                                                                                       aaTTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTttatta             <  1:535747/141‑1 (MQ=255)                                                                                                                        attattAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTTtattat            >  1:365588/1‑141 (MQ=255)                                                                                                                        attattAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTTtattat            >  1:785610/1‑141 (MQ=255)                                                                                                                          tattaGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTTTATTATAg          <  2:516473/141‑1 (MQ=255)                                                                                                                             taGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTTTATTATAGaaa       <  2:562651/141‑1 (MQ=255)                                                                                                                                 tACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTTTATTATAGAAAGGTc   <  1:706329/141‑1 (MQ=255)                                                                                                                                  aCAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTTTATTATAGAAAGGTcc  >  2:768305/1‑141 (MQ=255)                                                                                                                                       |                                                                                                                                        GTGATGATTATGTTGATTTCTAAAAAAGAATCAAAAGAAACAACACATAAGGACGATGAGTATATTTATCATTAATATGTTCATAGCAAAAGAAAAACCATTAAAATGTTAAGTTGTTAATTATTAGATACAACCAACATTTTAATGGTTTTATTTTTAACTTTGTAGTTCTTGGAATGTTTGAACGATTAAATAGACATTTAAAATACTTAGAATAATAATAAGTGTCCATGAAATGATATTAACCCATGTTTTATTATAGAAAGGTCC  >  CP000730/1113997‑1114266

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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.