New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1205383 =	105 (0.920)	27 (0.290) +TTCCTAGGGTGCCGTCTCAGCCTTG	6/226	15.6	30.1%	intergenic (‑264/‑305)	USA300HOU_RS15290/lspA	hypothetical protein/Lipoprotein signal peptidase
	?	USA300TCH1516_ALE	2478476 =	48 (0.420)					intergenic (+363/‑212)	USA300HOU_RS12760/USA300HOU_RS12765	hypothetical protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.

ATGCCCATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACAAAT  >  USA300TCH1516_ALE/2478336‑2478615                                                                                                                                             |                                                                                                                                            aTGCCCATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCCACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTg                                                                                                                                             <  4:44105/141‑1 (MQ=25)    cccATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCt                                                                                                                                          <  1:239043/141‑1 (MQ=35)    cccATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCt                                                                                                                                          <  3:331545/141‑1 (MQ=35)       aTCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCg                                                                                                                                       <  3:150525/141‑1 (MQ=33)        tCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGa                                                                                                                                      >  1:386473/1‑141 (MQ=32)        tCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGa                                                                                                                                      >  2:746142/1‑141 (MQ=32)            gCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTgg                                                                                                                                  <  2:858789/141‑1 (MQ=11)                                                                          tctcAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTaaa                                                                    >  3:326891/1‑141 (MQ=32)                                                                             cAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATAc                                                                 >  2:538976/1‑141 (MQ=32)                                                                               gCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACtt                                                               >  2:699796/1‑141 (MQ=34)                                                                                 cACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTa                                                             <  1:62772/141‑1 (MQ=35)                                                                                   ccccAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTaaa                                                           >  1:99739/1‑141 (MQ=35)                                                                                       aaCCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATATTTTaaaaaaa                                                       >  1:249500/1‑141 (MQ=38)                                                                                       aaCCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTaaaaaaa                                                       >  1:104214/1‑141 (MQ=38)                                                                                       aaCCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTaaaaaaa                                                       >  1:38984/1‑141 (MQ=39)                                                                                            gCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGa                                                  <  4:246293/141‑1 (MQ=255)                                                                                              acaTTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGaca                                                >  1:772305/1‑141 (MQ=255)                                                                                               caTTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGacac                                               >  1:505749/1‑141 (MQ=255)                                                                                               caTTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGacac                                               <  4:362815/141‑1 (MQ=255)                                                                                                aTTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACt                                              <  2:329573/141‑1 (MQ=255)                                                                                                   gttgtAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTg                                           >  2:578300/1‑141 (MQ=255)                                                                                                    ttgtAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTgg                                          >  2:522163/1‑141 (MQ=255)                                                                                                        aaGCTGACTACATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCaa                                      <  3:156128/141‑1 (MQ=255)                                                                                                           cTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACtt                                   <  3:83482/141‑1 (MQ=255)                                                                                                                tataTNTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGcc                              <  3:143620/141‑1 (MQ=255)                                                                                                                tataTGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGcc                              >  4:148171/1‑141 (MQ=255)                                                                                                                 tatagTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCa                             >  1:93724/5‑141 (MQ=255)                                                                                                                    tGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGa                          >  2:308511/1‑141 (MQ=255)                                                                                                                    tGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGa                          <  2:270907/141‑1 (MQ=255)                                                                                                                       cAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATAc                       >  2:406425/1‑141 (MQ=255)                                                                                                                         gCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACaa                     >  2:330468/1‑141 (MQ=255)                                                                                                                         gCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACaa                     >  1:803512/1‑141 (MQ=255)                                                                                                                           ttCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAAtt                   <  4:232019/141‑1 (MQ=255)                                                                                                                             cTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTa                 >  1:192436/1‑141 (MQ=255)                                                                                                                              tgtgTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTAc                <  1:617043/141‑1 (MQ=255)                                                                                                                               gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACa               <  1:699796/141‑1 (MQ=255)                                                                                                                               gtgtTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCCCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTACGCCAGGATACAATTTACa               >  1:238878/1‑141 (MQ=255)                                                                                                                                  ttGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAAt            <  2:781904/141‑1 (MQ=255)                                                                                                                                     gggCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGGCTCGCCATTAAGAGTACGTATTAACATGTATTTTTGCTTTTAAAGACTTTAAGAAAATAAGACACTGTGGCCAACTTAAGCCAGGATACAATTTAGAAGTAgg         >  4:84845/1‑140 (MQ=17)                                                                                                                                      ggCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCg        <  2:217962/141‑1 (MQ=255)                                                                                                                                      ggCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCg        >  1:659896/1‑141 (MQ=255)                                                                                                                                      ggCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCg        <  1:41365/141‑1 (MQ=255)                                                                                                                                       gCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGa       >  3:300715/1‑141 (MQ=255)                                                                                                                                       gCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGa       >  1:556423/1‑141 (MQ=255)                                                                                                                                       gCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGa       >  4:261602/1‑141 (MQ=255)                                                                                                                                        ccccTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGAc      <  1:545596/141‑1 (MQ=255)                                                                                                                                         cccTGTCTTCTACTGGCATTGCTCCCTCAGGTGTCTCGCCACTAATACTACGTATTAACATGTAATTTTACTTTTTAATACTTTAAAAACATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACa     >  4:53872/1‑141 (MQ=18)                                                                                                                                         cccTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACa     <  3:198450/141‑1 (MQ=255)                                                                                                                                            ggTCTTCGACTGTCACTTCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACAAAt  <  2:780204/140‑1 (MQ=255)                                                                                                                                             |                                                                                                                                            ATGCCCATCTGGCACATTACTGTAAAATTCTATAAATAGAATTTTTGATGACGGGTCCCTTCCTAGGGTGCCGTCTCAGCCACCCCAACCGGCACATTGTTGTAAGCTGACTATATGTCAGCTTCTGTGTTGGGGCCCCTGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTAAATACTTTAAAAAAATAAGACACTTTGGCCAACTTAAGCCAGGATACAATTTACAAATAGCGACAAAT  >  USA300TCH1516_ALE/2478336‑2478615

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