New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2857675 =	139 (0.990)	3 (0.020)	3/238	NT	2.3%	intergenic (+71/‑172)	nixA/nhoA	High‑affinity nickel‑transport protein NixA/N‑hydroxyarylamine O‑acetyltransferase
	?	USA300TCH1516_ALE	2857737 =	125 (0.970)					intergenic (+133/‑110)	nixA/nhoA	High‑affinity nickel‑transport protein NixA/N‑hydroxyarylamine O‑acetyltransferase
Rejected: Frequency below/above cutoff threshold.

AAGATTATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGCGTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2857824‑2857675 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgagagcgtaTTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAATTATTT  >  USA300TCH1516_ALE/2857737‑2857875                                                                                                                                                                                                                                                                                                   AAGATTATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACT                                                                                                                                                      <  1:157249/141‑1 AAGATTATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACT                                                                                                                                                      >  2:774879/1‑141 AAGATTATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACT                                                                                                                                                      <  1:761229/141‑1 AAGATTATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACT                                                                                                                                                      >  1:654620/1‑141 AAGATTATAATTAAATTTTAAACAGAAATACTGAAATTGTAAATTCGAAAGCATTGAACTTTGGATAAATACATTTTAAATAGAAACATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACT                                                                                                                                                      <  4:379856/141‑1  AGATTATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTG                                                                                                                                                     >  2:18769/1‑141    ATTATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAG                                                                                                                                                   >  1:1004645/1‑141       ATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGC                                                                                                                                                >  1:679012/1‑141       ATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGC                                                                                                                                                >  2:192444/1‑141        TAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGCG                                                                                                                                               <  3:353697/141‑1         AATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGCGT                                                                                                                                              >  2:385635/1‑141          ATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGCGTA                                                                                                                                             >  4:143141/1‑141          ATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGCGTA                                                                                                                                             >  3:297275/1‑141                                                                                  AGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGCGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAA                                                                     >  1:795246/1‑141                                                                                         TACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGCGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAAT                                                              >  2:961155/1‑141                                                                                                               CTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGCGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGC                                        <  2:795246/141‑1                                                                                                                                              GAGAGCGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGA         <  2:865177/141‑1                                                                                                                                              GAGAGCGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGAGCTATGCTTATGAATATTGCGAAGTTAGAGA         <  2:665881/141‑1                                                                                                                                               AGAGCGTATTTTTTTTTTTTTTTTGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAA        >  2:1030852/1‑141                                                                                                                                               AGAGCGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAATTTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAGGTTAGAGAA        >  2:453458/1‑141                                                                                                                                               AGAGCGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAA        >  2:720914/1‑141                                                                                                                                               AGAGCGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAA        >  1:486295/1‑141                                                                                                                                               AGAGCGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAA        >  1:357589/1‑141                                                                                                                                                   CGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGATGTTAGAGAATTAT    >  3:246581/1‑141                                                                                                                                                   CGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAATTAT    <  1:347030/141‑1                                                                                                                                                   CGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAATTAT    <  2:879188/141‑1                                                                                                                                                   CGTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAATTAT    >  3:362717/1‑141                                                                                                                                                    GTATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAATTATT   >  1:761874/1‑141                                                                                                                                                     TATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAATTATTT  <  1:447237/141‑1                                                                                                                                                     TATTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAACTTAATTATAATCTTGAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAATTATTT  <  1:86853/141‑1                                                                                                                                                                                                                                                                                                   AAGATTATAATTAAATTTTAAACAGAAATACTGAAATTTTAAATTCGAAAGCATTGAATTTTGGATAAATACATTTTAAATAGAAAAATACGCTCTCAAAATGAAGTCATCTCTAAAAGAAACGATTTAAAGATGACTACTGAGAGCGTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2857824‑2857675 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tgagagcgtaTTTTTCTATTTAAAATGTATTTATCCAAAATTCAATGCTTTCGAATTTAAAATTTCAGTATTTCTGTTTAAAATTTAATTATAATCTTTAATACAGGAGGCGCTATGCTTATGAATATTGCGAAGTTAGAGAATTATTT  >  USA300TCH1516_ALE/2857737‑2857875

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.