New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	954695 =	166 (0.810)	32 (0.170) +GGCAAG	12/148	NT	15.5%	intergenic (+349/+154)	gluD/glpQ_1	NAD‑specific glutamate dehydrogenase/Glycerophosphodiester phosphodiesterase
	?	USA300TCH1516_ALE	1873938 =	213 (1.050)					intergenic (‑614/+136)	USA300HOU_RS09300/USA300HOU_RS09305	Putative dipeptidase/hypothetical protein

GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/954740‑954695 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCTTG  >  USA300TCH1516_ALE/1873938‑1873993                                               |||||||                                                           GGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTT                     <  2:2144104/91‑1 GGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTT                     <  1:2890500/91‑1 GGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTT                     <  1:2890642/91‑1 GGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTT                     <  1:2890871/91‑1 GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACTAGAATTGAAAATGCGCTTGTAACAAGCTTTTT                     <  1:3029679/91‑1 GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACTAGAATTGAAAATGCGCTTGTAACAAGCTTTTT                     <  1:32666/91‑1  GACAGAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATACGCTTGTAACAAGCTTTTTT                    <  2:2076300/91‑1   ACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTTTC                   <  1:524946/91‑1    CAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACTAGAATTGAAAATTCGCTTGTAACAAGCTTTTTTCA                  <  2:2812579/91‑1    CAGAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAAT                <  2:873426/91‑1     AGAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAGATACGCTTGTAACAAGCTTTTTTCAATT               <  2:3103145/91‑1     AGAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATT               <  2:2851821/91‑1     AGAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGAAG‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATT               <  1:3326404/91‑1     AGAAATCATATTTTAGCAAAAGTTATTTCGTCGTCCCGCACCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATT               <  2:3103120/91‑1      GAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTC              <  2:1195268/91‑1      GAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTC              <  2:2426049/91‑1      GAAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTC              <  1:1649833/91‑1       AAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCT             <  2:3811964/91‑1       AAATCATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCT             <  2:1795323/91‑1        aatcATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTA            <  1:917110/87‑1        aatcATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTA            <  1:2907750/87‑1        aatcATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTA            <  1:115340/87‑1        AATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTA            <  2:2278661/91‑1          tcATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGT          <  1:1368470/89‑1            ATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑CGAAAATTCGCTTGTAACAAGCTTTTTTCAATTCTAGTCA        <  1:3349994/91‑1            ATATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCA        <  1:2502704/91‑1             TATTTTCGCAAAATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAA       <  1:1436451/91‑1             TATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCA‑AGGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCAA       <  2:2114434/91‑1              ATTTTAGCAAAATTTATTTCGTCGTCCCACCCCGGCAGTAGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCAA       <  2:943117/91‑1                 ttaGCAAAATTTATTTCGTCGTCCCACCCCGGCAGTAGTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCT    <  1:1935927/88‑1                  TCGCAAGATTTATTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCTTG  <  2:2739508/91‑1                  TCGCAAAATTTAGTTCGTCGTCCCACCCCAGCA‑AGGTTGACT‑GAA‑CGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCACCCTTG  <  2:2739459/91‑1                                               |||||||                                                           GGACAGAAATGATATTTTCGCAAAATTTATTTCGTCGTCCCACCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/954740‑954695 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTTGACT‑GAA‑TGAAAATACGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCTTG  >  USA300TCH1516_ALE/1873938‑1873993

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.