New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2476453	77 (0.780)	9 (0.110)	6/136	NT	10.7%	intergenic (‑198/+42)	tcaA/tcaR	Membrane‑associated protein TcaA/HTH‑type transcriptional regulator TcaR
	?	USA300TCH1516_ALE	= 2476476	85 (1.020)					intergenic (‑221/+19)	tcaA/tcaR	Membrane‑associated protein TcaA/HTH‑type transcriptional regulator TcaR

AGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2476352‑2476453 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gaaggtgttcaaATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAATTC  <  USA300TCH1516_ALE/2476476‑2476387                                                                                                                                                                                                  AGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAG                                                                                                       >  1:1780154/1‑91  GAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGA                                                                                                      <  1:2758048/91‑1      ACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGT                                                                                                  >  1:697344/1‑91        AATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGT                                                                                                >  1:534308/1‑91        AATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGT                                                                                                <  1:1066356/91‑1        AATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGT                                                                                                >  1:385999/1‑91        AATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGT                                                                                                <  1:3498297/91‑1        AATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGT                                                                                                <  1:2984720/91‑1         ATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTT                                                                                               <  1:3377624/91‑1           TCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCA                                                                                             >  1:155485/1‑91            CAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAA                                                                                            <  1:2126467/91‑1                                   AGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAAATATAAGACTAAATATGTATGTA                                                                     <  1:561372/91‑1                                    GAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAAATATAAGACTAAATATGTATGTAT                                                                    <  1:1905754/91‑1                                        TGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAAATATAAGACTAAATATGTATGTATTGAA                                                                <  1:2401670/91‑1                                        TGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAAATATAAGACTAAATATGTATGTATTGAA                                                                <  1:959777/91‑1                                          TACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAAATATAAGACTAAATATGTATGTATTGAACA                                                              <  1:3103412/91‑1                                           ACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAAATATAAGACTAAATATGTATGTATTGAACAC                                                             <  1:675169/91‑1                                           ACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAAATATAAGACTAAATATGTATGTATTGAACAC                                                             <  1:3914999/91‑1                                            CCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACC                                                            <  1:3610976/91‑1                                            CCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACC                                                            <  1:498312/91‑1                                                                                            AAGGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAA            >  1:2991148/1‑91                                                                                            AAGGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTCTTTAGTTATAATTGAGAGAGTACTTTCATCAATAATGTAATAA            >  1:4152530/1‑91                                                                                             AGGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAG           <  1:2518488/91‑1                                                                                              GGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGG          <  1:3101873/91‑1                                                                                              GGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGG          <  1:831858/91‑1                                                                                              GGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGG          >  1:1779625/1‑91                                                                                              GGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGG          >  1:546942/1‑91                                                                                              GGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGG          >  1:1147395/1‑91                                                                                              GGTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGG          >  1:511820/1‑91                                                                                               GTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGT         >  1:315505/1‑91                                                                                               GTGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGT         >  1:1723782/1‑91                                                                                                TGTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTA        >  1:3439088/1‑91                                                                                                 GTTCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTAC       <  1:1120941/91‑1                                                                                                   TCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAA     >  1:418757/1‑91                                                                                                   TCAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAA     >  1:418493/1‑91                                                                                                    CAAATATAATACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAAT    <  1:3978490/91‑1                                                                                                    CAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAAT    <  1:3976586/91‑1                                                                                                    CAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAAT    >  1:3674187/1‑91                                                                                                    CAAATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAAT    >  1:3674120/1‑91                                                                                                      AATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAATTC  <  1:2452615/91‑1                                                                                                      AATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAATTC  <  1:1793370/91‑1                                                                                                                                                                                                  AGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2476352‑2476453 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gaaggtgttcaaATATAAGACTAAATATGTATGTATTGAACACCTTCTTTTTAGTTATAATTGAGAGAGTACTTTCATAAATAATGTAATAAGGTACAATTC  <  USA300TCH1516_ALE/2476476‑2476387

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