New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000731	= 1526	45 (0.790)	4 (0.010) +TTG	4/250	7.7	1.4%	intergenic (+311/‑545)	repA/USA300HOU_pUSA300HOUMR0003	replication protein A/hypothetical protein
	?	NC_012417	= 997	548 (0.910)					intergenic (+9/+6)	USA300HOU_RS14890/USA300HOU_RS15665	replication protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGATGGTAATTTGATTAATACAAGTGATGAAGATAAAACGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACT  >  CP000731/1408‑1652                                                                                                                       |                                                                                                                               aGATGGTAATTTGATTAATACAAGTGATGAAGATAAAACGACAGACGAAGAAAAAAAACACATTCAATTACCGAAATTTGGAATTTCGAAAAACAAAATTAATATTTAAGACATTAATAATAACTCATg                                                                                                                      >  1:48525/1‑129 (MQ=14)   attgTAATTTGATTAATACAAGTGATTAAGATAAAACGACAGACTAAGAAAAAAAGCACATTCAATTACCGCAATTTGTAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTc                                                                                                                    <  2:69201/126‑1 (MQ=255)      gTAATTTGAGTAATACAAGTGAAGAAGATAAAACGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCttt                                                                                                                 <  1:6786/129‑1 (MQ=255)                     cAAGTGATGAAGATAAAACGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCt                                                                                                  <  2:181570/129‑1 (MQ=255)                       aGTGATGAAGATAAAACGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGt                                                                                                <  2:160514/129‑1 (MQ=255)                         tgatgaAGATAAAACGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTaa                                                                                              <  1:112271/129‑1 (MQ=255)                                 aTAAAACGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGATAATCATATTTATTATTTTAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGc                                                                                      <  1:24996/129‑1 (MQ=18)                                 aTAAAACGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGc                                                                                      <  1:188536/129‑1 (MQ=255)                                 aTAAAACGAAAAATGAAGAAAAAAAGCACATTCAATTACCTCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGc                                                                                      <  2:232394/129‑1 (MQ=255)                                   aaaaCGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTg                                                                                    >  1:207438/1‑129 (MQ=255)                                    aaaCGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGt                                                                                   <  1:234783/129‑1 (MQ=255)                                    aaaCGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCAAAAAACAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGt                                                                                   >  1:76750/1‑129 (MQ=255)                                      aCGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCt                                                                                 >  1:201549/1‑129 (MQ=255)                                       cGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTTTAAAACAGTGCTGTCtt                                                                                >  2:112448/1‑129 (MQ=255)                                         aCAGACGAAGAAAAAAAGCACATTCAATTACCGTACGTAGTAATGTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTAt                                                                              <  1:98823/129‑1 (MQ=18)                                         aCAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTAt                                                                              >  1:165367/1‑129 (MQ=255)                                           aGACGAAGAAAAAAAGCACATTCAATTACCGCAATGTGCAATTGTGATGAGCCATTCAAATTTCTTAGACATTAGTGATAACCGATGTCTTTTTTTATTGTTTTCATCTAAAAAAGTCCCACCTTAttt                                                                            >  2:205287/1‑129 (MQ=12)                                             aCGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTAttttt                                                                          <  2:52728/129‑1 (MQ=255)                                             aCGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTCCTGTCTTAttttt                                                                          <  2:178699/129‑1 (MQ=255)                                               gaagaaAAAAAGCACATTCAATTACTGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAATACATTAGTGATATTTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTtgt                                                                        <  1:85794/129‑1 (MQ=255)                                                aagaaAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTtgtg                                                                       <  2:137314/129‑1 (MQ=255)                                                 agaaAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGa                                                                      >  2:67850/1‑129 (MQ=255)                                                  gaaAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTtgtagt                                                                     >  1:169846/1‑126 (MQ=255)                                                    aaaaaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAATACATTAGTGGTAACTGATGTTTTTTTTTATTGTTTTTCTGTAAAAAAGTGCGGTCTTATTTTTGTGACaa                                                                   <  1:12376/129‑1 (MQ=255)                                                      aaaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGTCAAAt                                                                 >  2:168646/1‑129 (MQ=255)                                                      aaaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAAt                                                                 >  1:210758/1‑129 (MQ=255)                                                      aaaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGAAAAGTGATGTAATTATTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAAt                                                                 >  1:183934/1‑129 (MQ=17)                                                         aGCACATTCTATGACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCt                                                              <  2:125828/129‑1 (MQ=255)                                                         aGCACATTCAATTACCGCAATTTGGAATTTCGAAAAAAAAAAATATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAGAAGTGCTGTCTTATTTTTGTGACAAATGCt                                                              >  1:115799/1‑129 (MQ=255)                                                                tCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGAGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCtgtatgta                                                       >  1:225377/1‑129 (MQ=255)                                                                 gaaTTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAg                                                      <  2:60604/128‑1 (MQ=255)                                                                   aTTACCGTAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTTTTTTTGTGACAAATGCTGTATGTAgtg                                                    <  2:208283/129‑1 (MQ=255)                                                                   aTTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTATGTAATCGAAAAAAACTTTTGTTTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGGCTTATTTTTGTGACAAATGCTGTATGTAgtg                                                    <  1:223258/129‑1 (MQ=17)                                                                       cagCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAATAAAGTGCTGTCTTATTTTTGTGACAAAGGCTGTATGTAGTGTcac                                                <  1:68550/127‑1 (MQ=255)                                                                         gCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACaa                                              >  1:170109/1‑129 (MQ=255)                                                                               tGGAATTTTGAAATGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAgtgt                                        <  2:47230/129‑1 (MQ=255)                                                                                    tttCGAAAATCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGacac                                   <  2:62773/129‑1 (MQ=255)                                                                                    tttCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGacac                                   <  2:12119/129‑1 (MQ=255)                                                                                    tttCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAAATGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGacac                                   >  1:118838/1‑129 (MQ=255)                                                                                     ttCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACt                                  <  2:201549/129‑1 (MQ=255)                                                                                       cGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTATTTATCTGTAACCATGACCATGCAGATATTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTAc                                >  1:109328/1‑129 (MQ=18)                                                                                                             aGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAGAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTa          <  2:72050/129‑1 (MQ=255)                                                                                                               aCATTAGTGATAACTGATGTCTTTTTGTATTTGTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTaaa        <  2:127406/129‑1 (MQ=255)                                                                                                                 aTTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAAt      <  2:22628/129‑1 (MQ=255)                                                                                                                     ttGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTTCTTACTTATTTTTGTGACAAATTCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACt  <  2:208697/128‑1 (MQ=37)                                                                                                                       |                                                                                                                               AGATGGTAATTTGATTAATACAAGTGATGAAGATAAAACGACAGACGAAGAAAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAGTGTGACACTACAGCTTTGTATGATATCACTTTAAAATAACT  >  CP000731/1408‑1652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.