New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	811555 =	42 (1.100)	4 (0.110)	3/262	6.2	8.8%	intergenic (+160/‑117)	USA300HOU_0757/USA300HOU_0758	hypothetical protein/hypothetical protein
	?	CP000730	= 2664960	43 (1.190)					intergenic (+195/‑283)	pat/USA300HOU_2519	acetyltransferase/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ACAAGCCAACATATAAAATTTTAAACTTCTCAGGGGAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCAAAAAGCTTGTTACAAGCGCATTTT  >  CP000730/2664821‑2665099                                                                                                                                            |                                                                                                                                            acaAGCCAACATATAAAATTTTAAACTTCTCAGGGGAGTGGGACAGAAATGATAAAGAGCCACTAATGAGTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTaaaa                                                                                                                                            >  2:34442/1‑141 (MQ=255)          cATATAAAATTTTAAACTTCTCAGGGGAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCAt                                                                                                                                   <  1:327740/141‑1 (MQ=255)              taAAATTTTAAACTTCTCAGGGGAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGa                                                                                                                               <  1:152204/141‑1 (MQ=255)                 aaTTTTAAACTTCTCAGGGGAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAAt                                                                                                                            <  1:221609/141‑1 (MQ=255)                    tttAAACTTCTCAGGGGAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACt                                                                                                                         >  1:124982/1‑141 (MQ=255)                     ttAAACTTCTCAGGGGAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTa                                                                                                                        <  1:127185/141‑1 (MQ=255)                             ttttttggAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATTTAGTGGTTCTTACACATTAGCCACATCTAATTTTTACTTAAAAATAGAAATACATGAGTAAAACTCATGCATAAGAATTACTAATTTCtat                                                                                                                >  2:21396/7‑141 (MQ=11)                               cAGGGGAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAg                                                                                                              >  1:153620/1‑141 (MQ=35)                                   ggtgtgtGACAGAAATGGTAAAGGGCTTCTAATGATTTAATATATAGTGATACTAACGCATTATCAAAAGCTAATAAAAAAAAAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGaaaa                                                                                                          <  2:62915/138‑1 (MQ=2)                                    gAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGaaaaa                                                                                                         >  1:330589/1‑141 (MQ=32)                                     aGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAg                                                                                                        <  1:141135/141‑1 (MQ=32)                                      gTGAGACAGAAATGATAAAGAGCCACTAATGATTTAATATGTAGTAGTTCTTACACATTAGCCACAAAAAAAAAAAAAAAAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGt                                                                                                       <  2:168281/141‑1 (MQ=11)                                           aCAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTc                                                                                                  <  2:28491/141‑1 (MQ=34)                                              gAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCttt                                                                                               >  1:407732/1‑141 (MQ=35)                                                  tGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTAtcg                                                                                           >  1:9866/1‑141 (MQ=35)                                                  tGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGCAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTAtcg                                                                                           >  2:90198/1‑141 (MQ=21)                                                   gATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTAtcgt                                                                                          >  2:290849/1‑141 (MQ=35)                                                       aaGAGCCACTAATGATTTATTATGGAGTGGTTCTTACACATGAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCgtcgtc                                                                                      >  2:295300/1‑141 (MQ=255)                                                        agagCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTcc                                                                                     <  1:253663/141‑1 (MQ=39)                                                                  aTGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACt                                                                           <  1:154861/141‑1 (MQ=35)                                                                  aTGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTAATGCATAAGAAAAACCAGTTTCTATAGAAAAAGTATTTCTGTATCGTCGTCCCACCCCAAca                                                                           <  2:206661/141‑2 (MQ=11)                                                                              gTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTg                                                               <  2:223695/141‑1 (MQ=40)                                                                                 gTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTAGTACCACCCCAACTCGAACATTATTGTaa                                                            >  1:400731/1‑141 (MQ=255)                                                                                   ggTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGcaggaaaaacggtat                                                          >  1:375052/1‑128 (MQ=255)                                                                                         tACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACtt                                                    >  2:104518/1‑141 (MQ=40)                                                                                           cacaTTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGAcgaaa                                                  <  2:56075/141‑5 (MQ=38)                                                                                           aacaTTAGCAAAAGATAACGTGTACTAAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAAAAACAAAAAAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACtttc                                                  <  2:21668/140‑2 (MQ=11)                                                                                             caTTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCg                                                >  2:13511/1‑141 (MQ=255)                                                                                              aTTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGt                                               <  1:104518/141‑1 (MQ=255)                                                                                                   ctgtggCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCt                                          >  1:106893/6‑141 (MQ=255)                                                                                                      caGCTAATGTGAACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATAACTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCt                                       <  2:10044/141‑1 (MQ=255)                                                                                                        gcgaaggtgtATTTAAAAATAGGGATACGTGAGTAAAACTCATGCATAAGAAAGACTAAGTTCTATAGAAAAAGTATTGCTTTGTCGTCTTCCCACCGCAACTCGCACAGTATTGTAAGCTGGCTTTTCGTCAGGTTCtgt                                     <  2:140604/135‑1 (MQ=14)                                                                                                        gCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCtgt                                     >  1:239098/1‑141 (MQ=255)                                                                                                                gtACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGc                             >  2:189973/1‑141 (MQ=255)                                                                                                                  aCTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGccc                           >  1:195742/1‑141 (MQ=255)                                                                                                                       aaaaTAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCaaaaa                      >  2:176177/1‑141 (MQ=255)                                                                                                                         aaTAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCAAAAAGc                    >  1:242914/1‑141 (MQ=255)                                                                                                                         aaTAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTATATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCAAAAAGc                    <  2:49903/141‑1 (MQ=255)                                                                                                                          aTAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCAAAAAGCt                   <  1:369190/141‑1 (MQ=255)                                                                                                                             ggAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCAAAAAGCTTGt                >  2:346259/1‑141 (MQ=255)                                                                                                                             ggAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCAAAAAGCTTGt                >  2:242698/1‑141 (MQ=255)                                                                                                                                    aTGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCAAAAAGCTTGTTACAAgc         <  1:132411/141‑1 (MQ=255)                                                                                                                                      gAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTGTATCGTCGTCGCACCCCAACTCGCTCATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCTCCAAAAGCTTGTTAGAAgcac       <  2:211130/141‑3 (MQ=17)                                                                                                                                           aaaCTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCAAAAAGCTTGTTACAAGCGCAtttt  >  1:377461/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                            ACAAGCCAACATATAAAATTTTAAACTTCTCAGGGGAGTGGGACAGAAATGATAAAGAGCCACTAATGATTTATTATGTAGTGGTTCTTACACATTAGCCACAGCTAATGTGTACTTAAAAATAGGAATACATGAGTAAAACTCATGCATAAGAAATACTAATTTCTATAGAAAAAGTATTTCTTTATCGTCGTCCCACCCCAACTCGCACATTATTGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCAAAAAGCTTGTTACAAGCGCATTTT  >  CP000730/2664821‑2665099

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.