New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1366496	118 (1.200)	8 (0.090)	6/152	NT	6.4%	intergenic (+72/‑85)	rpsN2/guaC	Alternate 30S ribosomal protein S14/GMP reductase
	?	USA300TCH1516_ALE	= 1366530	122 (1.310)					intergenic (+106/‑51)	rpsN2/guaC	Alternate 30S ribosomal protein S14/GMP reductase

GTTAAAAAATCAAGTTGGTAAAATCAAATTTCGTACTTTAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1366404‑1366496 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaacCGAATGTTTCCTTATTAATATGAGAAAACATTCAGTTTATAGCATTCGTATATACTGTACATTGTTTTATTGATATTGTAAATGGGCTAA  <  USA300TCH1516_ALE/1366530‑1366441                                                                                                                                                                                         GTTAAAAAATCAAGTTGGTAAAATCAAATTTCGTACTTTAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAA                                                                                              <  1:3163411/91‑1   TAAAAAATCAAGTTGGTAAAATCAAATTTCGTACTTTAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAAC                                                                                            >  1:51216/1‑91                          AAATTTCGTACTTTAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAACTGAATGTTTCCTTATTAATATGA                                                                     <  1:1461339/91‑1                                   ACTTTAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAACTGAATGTTTCCTTATTAATATGAGAAAACATT                                                            <  1:3747826/91‑1                                   ACTTTAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAACCGAATGTTTCCTTATTAATATGAGAAAACATT                                                            <  1:64877/91‑1                                     TTTAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAACTGAATGTTTCCTTATTAATATGAGAAAACATTCA                                                          <  1:3926829/91‑1                                       TAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAACCGAATGTTTCCTTATTAATATGAGAAAACATTCAGT                                                        <  1:2232512/91‑1                                       TAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAACCGAATGTTTCCTTATTAATATGAGAAAACATTCAGT                                                        <  1:2232514/91‑1                                         GCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAACCGAATGTTTCCTTATTAATATGAGAAAACATTCAGTTT                                                      <  1:133488/91‑1                                           CCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAACCGAATGTTTCCTTATTAATATGAGAAAACATTCAGTTTAT                                                    <  1:3580384/91‑1                                                                                             CCGAATGTTTCCTTATTAATATGAGAAAACATTCAGTTTATAGCATTCGTATATACTGTACATTGTTTTATTGATATTGTAAATGGGCTAA  <  1:1353450/91‑1                                                                                                                                                                                         GTTAAAAAATCAAGTTGGTAAAATCAAATTTCGTACTTTAGCCCATTTACAATATCAATAAAACAATGTACAGTATATACGAATGCTATAAAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1366404‑1366496 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaacCGAATGTTTCCTTATTAATATGAGAAAACATTCAGTTTATAGCATTCGTATATACTGTACATTGTTTTATTGATATTGTAAATGGGCTAA  <  USA300TCH1516_ALE/1366530‑1366441

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