New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	954695 =	155 (0.810)	51 (0.290) +GGCAAG	11/148	NT	24.7%	intergenic (+349/+154)	gluD/glpQ_1	NAD‑specific glutamate dehydrogenase/Glycerophosphodiester phosphodiesterase
	?	USA300TCH1516_ALE	1873938 =	181 (0.950)					intergenic (‑614/+136)	USA300HOU_RS09300/USA300HOU_RS09305	Putative dipeptidase/hypothetical protein

GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/954740‑954695 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCTTGCC  >  USA300TCH1516_ALE/1873938‑1873995                                               |||||||                                                             GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACTAGAATTGAAAATGCGCTTGTAACAAGCTTTTT                       <  1:214503/91‑1  GACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTTT                      <  1:169522/91‑1  GACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTTT                      <  1:169567/91‑1  GACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTTT                      <  2:3819363/91‑1  GACAGAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATACGCTTGTAACAAGCTTTTTT                      <  2:1512788/91‑1    CAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTTTCA                    <  2:1597362/91‑1    CAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAAT                  <  1:2371106/91‑1    CAGAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAAT                  <  1:231737/91‑1    CAGAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAAT                  <  1:231804/91‑1      GAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTC                <  1:1167195/91‑1      GAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTC                <  2:1343219/91‑1       AAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCT               <  2:805480/91‑1       AAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCT               <  2:2639626/91‑1       AAATGATATGTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTTTCAATT                 <  2:136710/91‑1       AAATCATGTTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCT               <  2:3454155/91‑1        aatcATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTA              <  1:749674/87‑1        AATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGACA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTA              <  2:3357860/91‑1        AATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTA              <  2:1424903/91‑1        AATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTA              <  2:2052665/91‑1        AATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTA              <  1:2364825/91‑1         ATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAG             <  1:1629013/91‑1         ATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAG             <  2:1949481/91‑1          TGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGT            <  1:640007/91‑1          TGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGT            <  1:3576447/91‑1          TGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGT            <  1:3576024/91‑1          TGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGT            <  1:3575868/91‑1          TGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGT            <  2:2436375/91‑1          TGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGT            <  2:3788954/91‑1          TGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGT            <  2:2436284/91‑1          TGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGT            <  1:1615936/91‑1          TGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGT            <  1:3631923/91‑1           GATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGTC           <  1:3264891/91‑1           GATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGCAACAAGCTTTTTTCAATTCTAGTC           <  2:836682/91‑1           GATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTC           <  2:2341882/91‑1           GATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTC           <  2:1408869/91‑1           GATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTC           <  2:745865/91‑1            ATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGTCA          <  2:2638704/91‑1            ATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGTCA          <  2:60401/91‑1            ATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCA          <  1:1841182/91‑1            ATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCA          <  2:1777293/91‑1            ATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCA          <  2:601656/91‑1             cATTCTCGCACAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCtc         <  2:2132283/90‑3             TATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAA         <  2:1192762/91‑1             TATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAA         <  1:546328/91‑1             TATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAA         <  2:3016607/91‑1              ATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAGTAGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAA         <  2:434305/91‑1                tttaGCAAAATTTATTTCGTCGTCCCACCCCGGCAGTAGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTGAATTCTAGTCAACC       <  2:3293700/87‑1                TTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCT      <  2:3172866/91‑1                 TTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAGTAGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCT      <  1:3508608/91‑1                  taGCAAAATTTATTTCGTCGTCCCACCCCGGCAGTAGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCTT     <  2:90063/89‑1                     tAAAATTTATTTCGTCGTCCCACCCCGGCAGTAGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCTTGCC  <  2:2768507/90‑1                                               |||||||                                                             GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/954740‑954695 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCTTGCC  >  USA300TCH1516_ALE/1873938‑1873995

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